PhD Journey

28/12/2025

A terrifying discovery confirms the fungus Candida auris is adapting.
It uses a CO2-based metabolic strategy to thrive on human skin by cooperating with specific skin bacteria to generate energy and neutralize antifungal therapies. Specialized antibacterial washes are now the only way to curb this hospital super-pathogen.

Shared for informational purposes only.
Source: Medical University of Vienna

28/08/2025

Check this out—how Candida auris diversifies its population!

White-Brown switching controls phenotypic plasticity and virulence of Candida auris

http://dlvr.it/TMkJgC

19/10/2024

👋 "Fifty shades of Brown" in Candida auris
🪶 là một tác nhân gây dịch kéo dài tại nhiều bệnh viện, viện dưỡng lão trên khắp thế giới mặc dù chỉ mới xuất hiện từ năm 2009. Khả năng bám dính tốt, đa đề kháng với thuốc kháng nấm và sự đa dạng về kiểu hình lâm sàng khiến auris được liệt kê như tác nhân ưu tiên chú ý bởi World Health Organization (WHO). WGS của hơn 10000 chủng đã được công bố trên NCBI, tuy nhiên sự đa dạng di truyền giữa các chủng ở mức hạn chế, khó giải thích được tính đa dạng và thay đổi nhanh chóng của loài này trong quá trình điều trị. Để làm tiền đề cho các công bố tiếp theo, chúng tôi thảo luận về biến thể nội loài và sự liên kết với hiện tượng di truyền biểu sinh (epigenetics) phát hiện gần đây trong lab "Multi-stable cell fate White-Brown switching" trên PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1012559

10/05/2024

🌡 Today's troubling news reports a record-breaking increase in CO2 levels in the world's atmosphere. This development makes even more dangerous, as evolutionary selection has endowed this fungal pathogen with an efficient trait: CO2 fixation.

✅ Check our preprint to learn how C. auris utilizes CO2 to deal with stress during environmental and host adaptation.

🏷 Link: https://www.biorxiv.org/content/10.1101/2024.04.12.589292v1


https://www.theguardian.com/environment/article/2024/may/09/carbon-dioxide-atmosphere-record

Experts issue warning after finding global average concentration in March was 4.7ppm higher than same period last year

17/09/2022

Prior to the SARS-CoV-2 pandemic, antibiotic resistance was listed as the major global health care priority. Some analyses, including the O’Neill report, have predicted that deaths due to drug-resistant bacterial infections may eclipse the total number of cancer deaths by 2050. Although fungal infections remain in the shadow of public awareness, total attributable annual deaths are similar to, or exceeds, global mortalities due to malaria, tuberculosis or HIV. The impact of fungal infections has been exacerbated by the steady rise of antifungal drug resistant strains and species which reflects the widespread use of antifungals for prophylaxis and therapy, and in the case of azole resistance in Aspergillus, has been linked to the widespread agricultural use of antifungals. This review, based on a workshop hosted by the Medical Research Council and the University of Exeter, illuminates the problem of antifungal resistance and suggests how this growing threat might be mitigated.

The impact of fungal infections on human health has been exacerbated by the rise of antifungal drug resistance. In this Review, the authors outline the problem of antifungal resistance and suggest how this growing threat might be mitigated.

01/09/2022

The 1st Scientific Seminar of Young Vietnamese Intellectuals on VTV4.

I presented my current work at the 1st Scientific Seminar of Young Vietnamese Intellectuals in Europe organized by Vietnamese Youth and Student Federation in Europe.

29/08/2022

Our protocol book chapter was released on Springer.

Candida albicans is a normal component of the human microflora that colonizes mucosal/epithelial surfaces and the gastrointestinal tract as a commensal organism. However, in an immunocompromised host, it can cause life-threatening infections of high mortality and...

21/08/2022

Aspergillus and Candida auris are becoming harder to treat with drugs common used for such infections.

Two types of fungi, Aspergillus and Candida auris, are becoming harder to treat with the drugs commonly used for such infections.

20/08/2022

A shortcoming of the current biofilm model is that it does not account for non-surface-attached aggregates that are often observed in clinical or environmental settings. This review proposed an updated conceptual model for biofilm.

In this Review, Bjarnsholt and colleagues propose a revised conceptual model of the biofilm life cycle that encompasses the three major steps of biofilm formation — aggregation, growth and disaggregation — independently of surfaces, and initiation from single-cell planktonic bacteria, and thus r...

19/08/2022

Prof. Karl Kuchler presents our work at the Yeast Genetic Meeting 2022, at UCLA.

https://genetics-gsa.org/yeast-2022/

16/08/2022

Essential R packages for fungal guys

: Provides access to pathogen annotation resources available on EuPathDB databases
This package helps us to retrieve annotation data from EuPathDB.

: Tools for building SQLite-based annotation data packages
Databases for fungal pathogens were provided on different platforms; we need a way to make it compatible to input into other analysis packages. Annotation Forge is a robust tool for this task.

: Client to access AnnotationHub resources
The Bioconductor team wants to collect popular web resources into their package called AnnotationHub. This beneficial tool provides genomic and transcriptomic profiles for many applications.

: Interface to BioMart databases (i.e. Ensembl)
This tool provides a way to access BioMart (Ensembl) annotation database directly from R. This is very useful for querying annotation data from Ensembl.

: A universal enrichment tool for interpreting omics data
This package provides an interface for functional annotation using data from various sources. They also provide excellent functions to visualize enrichment results obtained from its analysis.

: A pile of (hopefully) useful R functions
This is a set of functions really helpful for host-pathogen interaction analysis.

15/08/2022

Our first story of echinocandin resistance is now available in mBio.

Transcriptomics and Phenotyping Define Genetic Signatures Associated with Echinocandin Resistance in Candida auris
https://journals.asm.org/doi/10.1128/mbio.00799-22

Candida auris emerged as a human fungal pathogen only during the past decade. Remarkably, C. auris displays high degrees of genomic diversity and phenotypic plasticity, with four major clades causing hospital outbreaks with high mortality and morbidity rates. C. auris can show clinical resistance to all classes of antifungal drugs, including echinocandins that are usually recommended as first-line therapies for invasive candidiasis. Here, we exploit transcriptomics coupled with phenotypic profiling to characterize a set of clinical C. auris isolates displaying pronounced echinocandin resistance (ECN-R). A hot spot mutation in the echinocandin FKS1 target gene is present in all resistant isolates. Moreover, ECN-R strains share a core signature set of 362 genes differentially expressed in ECN-R isolates. Among others, mitochondrial gene expression and genes affecting cell wall function appear to be the most prominent, with the latter correlating well with enhanced adhesive traits, increased cell wall mannan content, and altered sensitivity to cell wall stress of ECN-R isolates. Moreover, ECN-R phenotypic signatures were also linked to pathogen recognition and interaction with immune cells. Hence, transcriptomics paired with phenotyping is a suitable tool to predict resistance and fitness traits as well as treatment outcomes in pathogen populations with complex phenotypic diversity.