Mat Beale
@typemat12.bsky.social
Microbial (meta)genomics researcher @sangerinstitute
interested in genomic epidemiology and evolutionary dynamics of STIs/NTDs/AMR in complex samples. Views my own.
https://www.sanger.ac.uk/person/beale-mathew/
interested in genomic epidemiology and evolutionary dynamics of STIs/NTDs/AMR in complex samples. Views my own.
https://www.sanger.ac.uk/person/beale-mathew/
Reposted by Mat Beale
Fungal friends: The University of Minnesota is hiring a tenure track medical mycologist, with emphasis on emergence of pathogens, genomics and evolution!
www.nature.com/naturecareer...
www.nature.com/naturecareer...
New Assistant Professor: Tenure Track - Fungal Biology/Medical Mycology - Minneapolis, Minnesota job with University of Minnesota - Medical School | 12848307
About the Job: The Department of Microbiology & Immunology and the Institute on Infectious Diseases (UMIID) at the University of Minnesota Medical ...
www.nature.com
November 23, 2025 at 11:42 AM
Fungal friends: The University of Minnesota is hiring a tenure track medical mycologist, with emphasis on emergence of pathogens, genomics and evolution!
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Reposted by Mat Beale
Have you heard of the Sanger Prize? It is a three-month undergrad placement at the Institute, and applications are open.
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
November 20, 2025 at 10:55 AM
Have you heard of the Sanger Prize? It is a three-month undergrad placement at the Institute, and applications are open.
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Hear from our current Sanger Prize holder Beatriz Rodrigues Estevam, here ⤵️
https://sangerinstitute.blog/2025/11/20/unravelling-the-mysteries-of-the-worm-through-bioinformatics/
Reposted by Mat Beale
This #WAAW Don’t forget to get your awesome AMR abstracts submitted to join us in Hinxton to discuss AMR genomics, innovations in diagnostics,
therapeutics, and data analytics, and novel mechanisms of antimicrobial survival! #AMR2026
therapeutics, and data analytics, and novel mechanisms of antimicrobial survival! #AMR2026
Present your #AMR work at our dedicated forum for global researchers and practitioners! 🧫
🗓️ 23-25 March 2026
Submit abstract by 1 December 📩
Share #genomics and big data approaches for navigating the growing complexities in the AMR field.
📎bit.ly/3SWzJUm
#MicroSky #AMR2026
🗓️ 23-25 March 2026
Submit abstract by 1 December 📩
Share #genomics and big data approaches for navigating the growing complexities in the AMR field.
📎bit.ly/3SWzJUm
#MicroSky #AMR2026
November 19, 2025 at 6:00 PM
Reposted by Mat Beale
We're launching a new HIV training programme for primary care staff in Lambeth, Lewisham, & Southwark.
The programme aims to increase awareness of contemporary HIV issues and ensure practitioners are able to make appropriate referrals.
www.thelovetank.info/news/hiv-tra...
The programme aims to increase awareness of contemporary HIV issues and ensure practitioners are able to make appropriate referrals.
www.thelovetank.info/news/hiv-tra...
HIV and PrEP training for South London primary care staff — The Love Tank CIC
The Love Tank is launching a new HIV awareness and prevention training programme for primary care staff in Lambeth, Lewisham, and Southwark.
www.thelovetank.info
November 17, 2025 at 2:57 PM
We're launching a new HIV training programme for primary care staff in Lambeth, Lewisham, & Southwark.
The programme aims to increase awareness of contemporary HIV issues and ensure practitioners are able to make appropriate referrals.
www.thelovetank.info/news/hiv-tra...
The programme aims to increase awareness of contemporary HIV issues and ensure practitioners are able to make appropriate referrals.
www.thelovetank.info/news/hiv-tra...
Reposted by Mat Beale
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:55 PM
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Reposted by Mat Beale
Fabulous meeting in Zimbabwe @thruzim.bsky.social for PROMISE Trial
Investigating STI screening in 12,000 women in antenatal care thruzim.org/hiv-srh-1/promise
Great team across clinical, stats, economics, social science, genomics & basic science to allow us to tackle a wide range of questions
Investigating STI screening in 12,000 women in antenatal care thruzim.org/hiv-srh-1/promise
Great team across clinical, stats, economics, social science, genomics & basic science to allow us to tackle a wide range of questions
November 13, 2025 at 1:51 PM
Fabulous meeting in Zimbabwe @thruzim.bsky.social for PROMISE Trial
Investigating STI screening in 12,000 women in antenatal care thruzim.org/hiv-srh-1/promise
Great team across clinical, stats, economics, social science, genomics & basic science to allow us to tackle a wide range of questions
Investigating STI screening in 12,000 women in antenatal care thruzim.org/hiv-srh-1/promise
Great team across clinical, stats, economics, social science, genomics & basic science to allow us to tackle a wide range of questions
Reposted by Mat Beale
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes www.nature.com/articles/s41... #jcampubs
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes - Nature Methods
By developing a strategy of metagenomic coassembly and prioritizing divergent marker gene sequences, Bin Chicken efficiently recovers more than 77,000 microbial genomes with high novel diversity, ther...
www.nature.com
November 13, 2025 at 7:46 PM
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes www.nature.com/articles/s41... #jcampubs
Reposted by Mat Beale
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
2026-27 Project (Dyson & Mostowy & Knight) - MRC London Intercollegiate Doctoral Training Partnership Studentships
PHACTS: Unravelling PHAge-baCTeria-host immune dynamicS to inform phage therapy SUPERVISORY TEAM Supervisor Dr Zoe Dyson...
mrc-lid.lshtm.ac.uk
November 13, 2025 at 11:11 AM
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...
Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi - Nature Communications
In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...
www.nature.com
November 12, 2025 at 8:36 PM
#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...
Reposted by Mat Beale
Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology
www.cell.com/trends/micro...
www.cell.com/trends/micro...
November 12, 2025 at 2:10 AM
Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology
www.cell.com/trends/micro...
www.cell.com/trends/micro...
Reposted by Mat Beale
Lucky, I was not drinking my morning coffee while reading this.
November 2, 2025 at 12:43 PM
Lucky, I was not drinking my morning coffee while reading this.
Reposted by Mat Beale
In advance of our November issue, our latest editorial is now online
The next decade in #AMR: getting the basics right
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
The next decade in #AMR: getting the basics right
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
October 27, 2025 at 10:25 AM
In advance of our November issue, our latest editorial is now online
The next decade in #AMR: getting the basics right
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
The next decade in #AMR: getting the basics right
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
Reposted by Mat Beale
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs
October 23, 2025 at 5:20 AM
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs
Reposted by Mat Beale
Our new preprint covering the improvements we made to our respiratory metagenomic assay is out now:
www.medrxiv.org/content/10.1...
✅ Now implemented in 6 NHS hospitals
✅ Increased sensitivity
✅ Increased pathogen genome coverage
(1/3)
www.medrxiv.org/content/10.1...
✅ Now implemented in 6 NHS hospitals
✅ Increased sensitivity
✅ Increased pathogen genome coverage
(1/3)
Optimisation of whole cell human depletion provides increased sensitivity and microbial genome coverage from respiratory metagenomic assays
Metagenomics is being adopted worldwide as a laboratory developed test. We have previously reported a unified metagenomic method for the direct detection of microorganisms from respiratory samples, de...
www.medrxiv.org
October 20, 2025 at 10:35 AM
Our new preprint covering the improvements we made to our respiratory metagenomic assay is out now:
www.medrxiv.org/content/10.1...
✅ Now implemented in 6 NHS hospitals
✅ Increased sensitivity
✅ Increased pathogen genome coverage
(1/3)
www.medrxiv.org/content/10.1...
✅ Now implemented in 6 NHS hospitals
✅ Increased sensitivity
✅ Increased pathogen genome coverage
(1/3)
Reposted by Mat Beale
This remains the funniest way to hear about an internet outage, though.
October 20, 2025 at 8:41 AM
This remains the funniest way to hear about an internet outage, though.
Reposted by Mat Beale
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
We’re very excited to finally share our latest work:
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
October 17, 2025 at 5:27 AM
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
Reposted by Mat Beale
After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research
microbiologysociety.org/news/society...
microbiologysociety.org/news/society...
<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest
microbiologysociety.org
October 7, 2025 at 8:44 AM
After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research
microbiologysociety.org/news/society...
microbiologysociety.org/news/society...
Reposted by Mat Beale
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
doi.org
October 6, 2025 at 10:42 AM
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Reposted by Mat Beale
Avoiding US tech? Some European alts:
🇳🇴 Browser: Vivaldi
🇫🇷 Search: Qwant
🇫🇷 Music: Deezer
🇫🇷 Hosting: OVH
🇫🇮 Mobile OS: Jolla
🇩🇪 Maps: Here WeGo
🇩🇪 Translation: DeepL
🇳🇱 Design: Sketch
🇨🇭 Notes: Standard Notes
🇨🇭 Messenger: Threema
🇨🇭 Dev Tools: Sonar
https://proton.me/blog/european-tech-alternatives
🇳🇴 Browser: Vivaldi
🇫🇷 Search: Qwant
🇫🇷 Music: Deezer
🇫🇷 Hosting: OVH
🇫🇮 Mobile OS: Jolla
🇩🇪 Maps: Here WeGo
🇩🇪 Translation: DeepL
🇳🇱 Design: Sketch
🇨🇭 Notes: Standard Notes
🇨🇭 Messenger: Threema
🇨🇭 Dev Tools: Sonar
https://proton.me/blog/european-tech-alternatives
European alternatives to US tech | Proton | Proton
Take back control of your digital life with privacy-focused European alternatives to US Big Tech apps and services.
proton.me
October 4, 2025 at 3:53 PM
Avoiding US tech? Some European alts:
🇳🇴 Browser: Vivaldi
🇫🇷 Search: Qwant
🇫🇷 Music: Deezer
🇫🇷 Hosting: OVH
🇫🇮 Mobile OS: Jolla
🇩🇪 Maps: Here WeGo
🇩🇪 Translation: DeepL
🇳🇱 Design: Sketch
🇨🇭 Notes: Standard Notes
🇨🇭 Messenger: Threema
🇨🇭 Dev Tools: Sonar
https://proton.me/blog/european-tech-alternatives
🇳🇴 Browser: Vivaldi
🇫🇷 Search: Qwant
🇫🇷 Music: Deezer
🇫🇷 Hosting: OVH
🇫🇮 Mobile OS: Jolla
🇩🇪 Maps: Here WeGo
🇩🇪 Translation: DeepL
🇳🇱 Design: Sketch
🇨🇭 Notes: Standard Notes
🇨🇭 Messenger: Threema
🇨🇭 Dev Tools: Sonar
https://proton.me/blog/european-tech-alternatives
Reposted by Mat Beale
Modern plasmids have evolved through complex microevolution and fusion events into a distinct group of highly recombinogenic, multi-replicon, self-transmissible plasmids that now pose the highest risk to resistance dissemination, and therefore to human health.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
www.science.org
September 27, 2025 at 11:11 AM
Modern plasmids have evolved through complex microevolution and fusion events into a distinct group of highly recombinogenic, multi-replicon, self-transmissible plasmids that now pose the highest risk to resistance dissemination, and therefore to human health.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Mat Beale
Samples from 1917 have helped identify the genetic culprits responsible for the spread of treatment-resistant infections 🔎
By mapping plasmid evolution since the pre-antibiotic era, experts found that a minority of plasmids cause most of the multidrug resistance in the world 🧵
By mapping plasmid evolution since the pre-antibiotic era, experts found that a minority of plasmids cause most of the multidrug resistance in the world 🧵
September 26, 2025 at 9:09 AM
Samples from 1917 have helped identify the genetic culprits responsible for the spread of treatment-resistant infections 🔎
By mapping plasmid evolution since the pre-antibiotic era, experts found that a minority of plasmids cause most of the multidrug resistance in the world 🧵
By mapping plasmid evolution since the pre-antibiotic era, experts found that a minority of plasmids cause most of the multidrug resistance in the world 🧵
Reposted by Mat Beale
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
Thread 1/n
Reposted by Mat Beale
History repeats itself: more disappearing STIs from molecular target mutation 😬 Great 🕵️ work by @sarah1alexander.bsky.social and colleagues!
The @ukhsa.bsky.social STI Reference Lab has identified a strain of Neisseria gonorrhoeae which evades detection on the Cepheid Xpert CT/GC Assay.
Read more in our eurosurveillance article
www.eurosurveillance.org/content/10.2...
Read more in our eurosurveillance article
www.eurosurveillance.org/content/10.2...
Detection and characterisation of Xpert CT/NG assay Neisseria gonorrhoeae diagnostic escape mutants, England, June 2025
We report the timely detection of a strain of Neisseria gonorrhoeae which was confirmed as a diagnostic escape mutant on the Cepheid Xpert CT/NG assay in England in June 2025. The reason for assay failure was a likely recombination event with Neisseria meningitidis, which removed both assay target sites. Seven historical putative Xpert CT/NG assay diagnostic escape mutants were also identified following subsequent in silico screening of gonococcal genome collections, but currently there is no evidence of widespread circulation.
www.eurosurveillance.org
September 14, 2025 at 6:45 AM
History repeats itself: more disappearing STIs from molecular target mutation 😬 Great 🕵️ work by @sarah1alexander.bsky.social and colleagues!
Reposted by Mat Beale
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
September 6, 2025 at 2:54 PM
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....