Tahsin Khan

Persistence and spread of fluconazole-resistant Candida parapsilosis clinical isolates associated with increased ERG11 copies in Qatar Candida parapsilosis is one of the most common species associated with candidemia infections globally. Recently, the emergence of fluconazole-resistant (FLU-R) C. parapsilosis has become a significant...

Excellent work from Zhu and Yue, plus good team work from Drs, scientists in Qatar, Canada and Singapore. #Candida #azoles #CNV
www.microbiologyresearch.org/content/jour...

A tour de force in
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.

Congrats Zam and Viridian team on this tremendous resource!

The new method for finding recurrent variants, "EVOtRec", is much faster than phylogenetics-based tools and produces congruent results. EVOtRec is based on topological data analysis.

A new method I've contributed to for finding potentially high fitness recurrent variants in pandemic-scale genome datasets is online:
arxiv.org/abs/2106.07292

Looking forward to applying this in other contexts!

Distinct Virome and Bacteriome Profiles of Term and Preterm Placentas from African, Asian and European Women While the human placental microbiome has been extensively studied, information regarding the virome remains limited. The association between subclinical placental viral infections and spontaneous pret...

our preprint is out today, here we investigated virome and bacteriome profile of term and preterm placentas from UK, Bangladesh and South African women.

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

Virome Analysis Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes.

Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero

link.springer.com/protocol/10....

Effect of human urinary microenvironment and fluid flow on antibiotic and phage therapy efficacy against uropathogenic Escherichia coli Urinary tract infections (UTI) remain a major global health burden, with high recurrence despite antibiotic treatment. The escalating prevalence of antimicrobial resistance further compromises therape...

Very pleased to plug our latest preprint, lead author @microberamon.bsky.social - fantastic collaboration with labs of Dario Carugo (Oxford) and Martha Clokie (Leicester) https:// - and others #UTISKy #UTI #IDSky #MicroSky www.biorxiv.org/content/10.1101/2025.11.12.688052v1 more below👇🧵

Congratulations Zam🎉

Comparative genomics reveals diversity and taxonomic relationships among Clostridioides difficile phages | Microbiology Spectrum Clostridioides difficile is a significant healthcare concern due to its role in causing severe infections and its increasing resistance to antibiotics. Phages present a promising alternative to antibi...

Comparative genomics reveals diversity and taxonomic relationships among Clostridioides difficile phages | Microbiology Spectrum journals.asm.org/doi/10.1128/...

How the Vectors of Antibiotic Resistance Have Evolved - Professor Zamin Iqbal YouTube video by Milner Centre for Evolution

Podcast with me and @turiking.bsky.social for the @milnerevolution.bsky.social series, on plasmid evolution over the last 100 years, talking about our ( @cazares-adr.bsky.social , Nick Thomson, @sarah1alexander.bsky.social & co) recent paper www.science.org/doi/10.1126/...
youtu.be/Mzr3TD4ijs0?...

🧬 New #GenEpiBioTrain course!

Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)

Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.

Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky

Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

Generative design of novel bacteriophages with genome language models Many important biological functions arise not from single genes, but from complex interactions encoded by entire genomes. Genome language models have emerged as a promising strategy for designing biol...

One for you @brockhurstlab.bsky.social !
Functional phages, and cocktails that work (caveat - have only looked at abstract)
www.biorxiv.org/content/10.1...

The Atlas Blue Butterfly. Credit: Roger Vila / The Institute of Evolutionary Biology.

The Atlas blue butterfly evolved 229 chromosome pairs — the most of any animal — over 3 million years, enabling new research 🦋

https://www.sanger.ac.uk/news_item/the-tale-of-the-creature-with-the-most-chromosomes/

@rogervilalab.bsky.social @charlottewright.bsky.social @ibe-barcelona.bsky.social

Introducing The Art of Visualization with ggplot2 – Nicola Rennie I’ve written a book! This blog post gives a brief introduction to The Art of Visualization with ggplot2, a book of data visualization case studies showing the end-to-end process of building charts, st...

I've written a short blog post introducing "The Art of Visualization with ggplot2"!

This book is all about the end-to-end process of creating charts with #ggplot2 📊 including data wrangling, sketching, and styling your plots!

nrennie.rbind.io/blog/art-of-...

#RStats #DataViz #TidyTuesday

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health The human gut microbiome plays an important biological role in host health, yet over 60% of gut species remain uncultured and hence inaccessible to experimental manipulation. Here we analysed 11,115 h...

🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...

Name changes for fungi of medical importance, 2022–2024 | Journal of Clinical Microbiology Since fungal identification methods based on examination of morphological and phenotypic features are complicated by the astonishing diversity of organisms capable of causing human infections especial...

Name changes for fungi of medical importance, 2022–2024 | Journal of Clinical Microbiology journals.asm.org/doi/10.1128/...

The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....

🌡️ Fungi in a warming world: join our PhD on Candida auris evolution – thermal tolerance, immunity & antifungal resistance. Based at Exeter & Bristol, GW4 BioMed2 MRC DTP : www.exeter.ac.uk/study/fundin... #InfectiousDiseases #PhD #GW4 #Exeter #Bristol #MedicalMycology #AMR #ClimateChange

Why and how to set up a Bioinformatics Learning Lab (BILL)

From asfiston.bsky.social & colleagues in @plos.org #Computational #Biology | Why and how to set up a Bioinformatics Learning Lab (BILL) | #Bioinformatics #Education #OpenScience #OpenEducationalResources 🧬 🖥️ 🧪🔓CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...

Evolution and evolvability of rifampicin resistance across the bacterial tree of life | PNAS Predicting the ability of bacteria to develop antibiotic resistance is challenging, especially for the vast majority of species for which no experi...

Evolution and evolvability of rifampicin resistance across the bacterial tree of life www.pnas.org/doi/abs/10.1... #jcampubs

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...

On the biological meaning of the population pangenome The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool ...

On the biological meaning of the population pangenome: Trends in Microbiology www.cell.com/trends/micro...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

Our paper “Global dissemination of npmA mediated pan‑aminoglycoside resistance via a mobile element in Gram‑positive bacteria” is now in @natcomms.nature.com. Part of my freshly defended PhD, so doubly happy! 😄🎉

🧵 (1/14)

www.doi.org/10.1038/s414...

How and when organisms edit their own genomes - Nature Genetics This Review describes the changes that some organisms make to their own DNA sequences, linking many to common genetic mechanisms built around canonical DNA repair and to a set of functional circumstan...

New paper @natgenet.nature.com

nature.com/articles/s41...

Our most recent thinking on HYP effectors involves programmed shuffling of the parasite genome. This prompted us to review how and when organisms edit their own genomes

In so doing, Vincent made two important discoveries...

(1/3)

Universal versus targeted chlorhexidine and mupirocin decolonisation and clinical and molecular epidemiology of Staphylococcus epidermidis bloodstream infections in patients in intensive care in Scotl... In ICU settings with low MRSA incidence, the benefits of universal decolonisation should be balanced against the risks of selecting MRSE sequence types adapted for invasive and device-associated infec...

Excessive use of disinfectants
www.thelancet.com/journals/lan...
A study has, for the first time, revealed a strong and direct link between the rise of antibiotic-resistant bacteria and universal disinfection procedures applied to patients in intensive care units
medicalxpress.com/news/2025-06...

Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬
and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

The Global Failure Behind the H5N1 Ecological Crisis

We need to talk about our collective failure — as a global society — to prevent the dissemination of H5N1 into wild animal populations. This omission is striking, given the ecological catastrophe currently unfolding. The virus originated(1/6)

How to bring experimental evolution to the classroom Pupils of all ages can benefit from witnessing evolution in real time - and it’s now possible in schools, say this researcher from the University of Bath

Its here! Finally published. www.tes.com/magazine/tea...

Allelic variations and gene cluster modularity act as nonlinear bottlenecks for cholera emergence | PNAS The underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. The diarrheal disease c...

Allelic variations and gene cluster modularity act as nonlinear bottlenecks for #cholera emergence www.pnas.org/doi/10.1073/...