Well, that and putting viral and bacterial talks on completely different floors…

Applications are OPEN for the 𝗖𝗥𝗘𝗔𝗧𝗜𝗩𝗘 𝗙𝗲𝗹𝗹𝗼𝘄𝘀𝗵𝗶𝗽!

A unique opportunity to build clinical research capacity in sub-Saharan Africa through:
• Academic training (MSc via LSHTM)
• Hands-on research experience
• Industry exposure

🗓 Deadline: 29 May 2026
🔗 www.lshtm.ac.uk/study/fees-a...

Yes, he caught me with killer questions more than once (after apparently sleeping through most of my talk). A great loss!

Oh nothing, just a peer reviewed paper my colleagues found...
doi.org/10.1016/j.ma...
"1 mL of the mass killing of an ethnic group was opposed to 20 mL of the skin sample and unprotected to light for 7 min."

Even AI knows what's wrong here, but @elsevierconnect.bsky.social doesn't.

Huge thanks to all partners in MAGUS consortium, inc @lshtm.bsky.social @thruzim.bsky.social, Botswana Harvard HP, Kwame Nkrumah University of Science & Technology, Makerere UC Health Sciences, @sangerinstitute.bsky.social , and all participants. Additional thanks to collabs at NICD South Africa.

Spatial distribution of South African sublineages over time, according to macrolide resistance allele.

In South Africa, we observed a 10-year transition from macrolide sensitive local sublineages to imported macrolide resistant sublineages. These findings argue for removal of azithromycin from WHO treatment guidelines, and show the value of genomic surveillance.

Distribution of samples by country, showing presence of macrolide resistance alleles( A2058G, A2059G). B - distribution of genomes according to inferred sublineage localisation and resistance allele.

We looked at AMR, and macrolide resistance (which is super high globally) was 20% (10% excluding South Africa). African lineages were mostly macrolide sensitive, and most macrolide resistance was driven by importation of global sublineages.

Collapsed phylogeny (1 tip per sublineage) showing sample count and country distributions for African genomes. C - arc plot showing sublineage sharing between African countries.

We observed limited transmission between African countries – 18/25 African sublineages found in only 1 country, 6/25 in 2 countries, 1/25 in 4 countries. Clear that cataloguing diversity requires more samples & more countries

WGS Phylogeny of 1376 genomes, inferring ancestral states (continent). B - sankey diagram showing sublineages descending from African MRCAs.

African genomes are largely distinct from global, descending from 7 MRCAs. We defined 56 sublineages, 20 exclusive to Africa, 31 non-African, 5 shared. Sublineage detection and accumulation much higher in Africa than globally.

Spatiotemporal distribution of T. pallidum genomes in dataset, inc. Lineage proportion by country

There are now >1000 T. pallidum genomes from HICs but hardly any from LMICs. This is partly because samples are not collected due to WHO syndromic management. We established clinical pathways for surveillance of genital ulcers in 4 African countries and recovered WGS for 147 novel Tp genomes.

Pleased to share our new preprint on genomic epi of #treponema www.medrxiv.org/content/10.6... focusing on genomic diversity and transmission of #syphilis in Africa with @drmichaelmarks.bsky.social @sangerinstitute.bsky.social @thruzim.bsky.social and many others

Germ factories or immune boot camps? Infection and immunity in childcare settings | Clinical Microbiology Reviews SUMMARYChildcare outside the home is a common experience for many children in high-income countries. It is associated with an increase in the incidence of infectious diseases—not just for the child bu...

Have you ever wondered why children starting nursery/daycare pick up so many germs? I certainly did, and with a crack team of parent-scientists/clinicians, we set out to answer that question. Is childcare a germ factory or an immune bootcamp? journals.asm.org/doi/10.1128/...

Apply by 11th May to do a PhD @lshtm.bsky.social Work with epidemiologists, social scientists & modellers to understand quality of life measures in Syphilis and develop evidence on cost-effectiveness of interventions & public health strategies.

@thelovetankcic.bsky.social @joetucker.bsky.social

I assumed that email was academic spam using ukri’s name, because they quoted a random paper that was supposedly mine but was clearly wrong and from a completely different field.

Image from their link showing evidence of fabricated references

Holy smoke. What ultimately happened???

a group of goats standing in a grassy field looking at the camera Alt: a group of goats running towards the camera

I don't think that the reviewers asking me for higher animal numbers really understand how many 40 goats are. Do you know the CHAOS that comes with dealing with 40 GOATS in an experimental setting!
Mice people cannot comprehend.
3 goats alone ate a tarp, a clock, and 2 expensive accelerometers!

It's a bit last minute, but we have an RA/junior postdoc position available in my lab (closing Sunday). Please reach out if you're interested in developing and applying methods to analyse microbial genomes and metagenomes! careers.petermac.org/job/MELBOURN...

International Syphilis Symposium Webinar Series

Announcing launch of the International Syphilis Symposium Webinar Series.

The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.

First meeting 26th March this year: Register below.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

España da un paso adelante en la lucha contra las #EnfermedadesTropicalesDesatendidas con la creación de la Coalición Española de ETD.

#ISGlobal forma parte de esta iniciativa que une ciencia, sociedad civil e instituciones.

🟠 https://tinyurl.com/5v66t6yz

#WorldNTDDay

MRC instructs grant review boards to slash funding rates - Research Professional News Boards asked to recommend just three applications for funding, as BBSRC also suspends calls

MRC instructs grant review boards to slash funding rates.

Boards asked to recommend just three applications for funding, as BBSRC also suspends calls.

www.researchprofessionalnews.com/rr-news-uk-r...

The beating heart of a broken machine

📣 A peer reviewer used #AI to create a fake review with 6 self-citation prompts. But is s/he the only perpetrator in our system? In the year's first editorial, Angela Huttner explores the depths of the academic-industrial complex.

#IDSky #clinmicro #peerreview

https://ow.ly/juoW50Y05t6

I was just thinking that…

If you're interested, MGEN (senior) editor call still open 😊 we're a nice team and you'll join a not-for-profit, community-driven journal that puts great emphasis on scientific integrity! (2/2) 🧬💻 #MicroSky #IDSky #NativeInSTEM #BlackInMicro #MicrobiomeSky microbiologysociety.org/who-we-are/j...

Amber Barton on mass drug administration to eradicate yaws in Papua New Guinea - The Lancet Microbe in conversation with Phoebe Ashley-Norman of The Lancet Microbe speaks to Amber Barton about the neglected tropical disease, yaws. Efforts to eradicate yaws were first made in the 1950s through a WHO and UNICEF campaign t...

Also, author Amber Barton discusses this work with us in this linked podcast

www.buzzsprout.com/1794195/epis...

#IDSky #ClinMicro #yaws #Treponema #MDA #AMR #OpenAccess #OA

New research article

Effect of repeated mass drug administration on the transmission of #yaws: a retrospective genomic epidemiology study

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

#IDSky #ClinMicro #Treponema #MDA #AMR #OpenAccess #OA

@sangerinstitute.bsky.social

The image shows two box and whisker plots. The left hand plot shows the duration of peoples ulcers stratified by sub-lineage and demonstrates that one of these sub-lineages has a longer duration of ulcers than the others. The right hand plot shows the titre of treponemal antibodies stratified by sub-lineage and demonstrates that the same sub-lineage is also associated with much lower antibody titres than the others.

Out @lancetmicrobe.bsky.social & led @amberbarton.bsky.social We used WGS to look at Treponema population dynamics during community MDA for yaws tinyurl.com/bd6zu6xm

Intriguingly found sublineage associated w longer ulcer duration & lower antibody titres. Whether occurs in syphilis needs exploring

Genomics uncovers new ways to target chronic childhood disease By sequencing the bacteria that cause the neglected disease yaws, researchers have found that while mass treatment can be successful, it can cause resistant strains to develop. They suggest that publi...

Really pleased to see our work on yaws, and how mass drug administration shapes Treponema genomes, published in @lancetmicrobe.bsky.social!

sanger.ac.uk/news_item/genomics-uncovers-new-ways-to-target-chronic-childhood-disease/

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

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...