Malaka De Silva
@malakades.bsky.social
Postdoctoral researcher based at the University of Cambridge.
Reposted by Malaka De Silva
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
September 17, 2025 at 11:58 AM
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
Reposted by Malaka De Silva
Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli!
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria
Abstract. Targeted gene editing can be achieved using CRISPR–Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization f
academic.oup.com
September 10, 2025 at 1:02 PM
Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli!
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
Reposted by Malaka De Silva
“…we demonstrate that although human use may affect the prevalence and mobility of genomic resistance in clinical isolates, for most antibiotics, genomic resistance existed within the pangenomes of sampled pathogens prior to clinical introduction.”
Really neat stuff!
Really neat stuff!
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 1, 2025 at 6:13 PM
“…we demonstrate that although human use may affect the prevalence and mobility of genomic resistance in clinical isolates, for most antibiotics, genomic resistance existed within the pangenomes of sampled pathogens prior to clinical introduction.”
Really neat stuff!
Really neat stuff!
Reposted by Malaka De Silva
Is the era of microbial metagenomics over? Check out our new preprint on using species abundance distributions to predict plasmid maintenance in bacterial communities: arxiv.org/abs/2509.01695
Heterogeneity drives plasmid maintenance in large microbial communities
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material b...
arxiv.org
September 3, 2025 at 9:22 AM
Is the era of microbial metagenomics over? Check out our new preprint on using species abundance distributions to predict plasmid maintenance in bacterial communities: arxiv.org/abs/2509.01695
Reposted by Malaka De Silva
New preprint with my HFSP collaborators. Network structures for bacterial and plasmid interactions determine community structure and evolvability: doi.org/10.32942/X21...
The interplay between ecological networks drives host-plasmid community dynamics
doi.org
September 3, 2025 at 11:11 AM
New preprint with my HFSP collaborators. Network structures for bacterial and plasmid interactions determine community structure and evolvability: doi.org/10.32942/X21...
Reposted by Malaka De Silva
Plasmids can be lost from a bacterial community even under positive environmental selection: doi.org/10.1101/2025...
Species interactions determine plasmid persistence in a 3-member bacterial community
Microbial communities are shaped by complex forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community respo...
doi.org
September 3, 2025 at 7:21 PM
Plasmids can be lost from a bacterial community even under positive environmental selection: doi.org/10.1101/2025...
Reposted by Malaka De Silva
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
🚨 New preprint! 🧬
𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.
We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use
📖 www.biorxiv.org/content/10.1...
𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.
We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use
📖 www.biorxiv.org/content/10.1...
Efficient detection and typing of phage-plasmids
Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...
www.biorxiv.org
September 3, 2025 at 2:00 PM
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
Reposted by Malaka De Silva
Vacancy! We have a postdoc position at UEA to explore the microbiology of metal resistance in Gram-positive pathogens.
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mrssbd7f
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social @femsmicro.org @norwichmicro.bsky.social
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mrssbd7f
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social @femsmicro.org @norwichmicro.bsky.social
Senior Research Associate (RA2346) in University of East Anglia | UEA
View details and apply for this Senior Research Associate (RA2346) vacancy in University of East Anglia. Faculty of Science
School of Biological Sciences
Senior Research Associate
Ref: RA23...
tinyurl.com
September 4, 2025 at 10:29 AM
Vacancy! We have a postdoc position at UEA to explore the microbiology of metal resistance in Gram-positive pathogens.
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mrssbd7f
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social @femsmicro.org @norwichmicro.bsky.social
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mrssbd7f
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social @femsmicro.org @norwichmicro.bsky.social
Reposted by Malaka De Silva
Vacancy! We have a Technician role at UEA to support research on metal resistance in Gram-positive pathogens.
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mr3ev3ke
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social
@femsmicro.org @norwichmicro.bsky.social
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mr3ev3ke
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social
@femsmicro.org @norwichmicro.bsky.social
Research Technician (TC923) in University of East Anglia | UEA
View details and apply for this Research Technician (TC923) vacancy in University of East Anglia. Faculty of Science
School of Biological Sciences
Research Technician (Part-Time, 0.6 FTE)
R...
tinyurl.com
September 4, 2025 at 10:31 AM
Vacancy! We have a Technician role at UEA to support research on metal resistance in Gram-positive pathogens.
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mr3ev3ke
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social
@femsmicro.org @norwichmicro.bsky.social
📍 Norwich UK
🗓️ Apply by 21st September 25
🔗 tinyurl.com/mr3ev3ke
RPs appreciated!
@microbiologysociety.org @asm.org @aussocmic.bsky.social
@femsmicro.org @norwichmicro.bsky.social
Reposted by Malaka De Silva
How should #XDR #shigellosis cases be treated? Our new education piece at #BMJ #SexuallyTransmittedInfections explores specific empirical treatment. Our recommendations are subsequent to our microbial genomic, phenotypic #AMR, and clinical/pharmacological analyses. sti.bmj.com/content/earl... 🧫💻🛟🧪🧬🦠
Antimicrobial treatment options for extensively drug-resistant (XDR) shigellosis in men who have sex with men
The sexual transmission of Shigella s onnei and Shigella flexneri has been observed since the 1970s between men who have sex with men (MSM) associated with living with HIV, sexually transmitted infect...
sti.bmj.com
August 28, 2025 at 6:07 PM
How should #XDR #shigellosis cases be treated? Our new education piece at #BMJ #SexuallyTransmittedInfections explores specific empirical treatment. Our recommendations are subsequent to our microbial genomic, phenotypic #AMR, and clinical/pharmacological analyses. sti.bmj.com/content/earl... 🧫💻🛟🧪🧬🦠
Reposted by Malaka De Silva
232 days to go ...
August 30, 2025 at 9:18 AM
232 days to go ...
Reposted by Malaka De Silva
August 13, 2025 at 6:39 AM
Reposted by Malaka De Silva
Why not follow our @shigellameeting.bsky.social starterpack of people who are speaking at and attending the conference - please message to be added to the starter pack if you're planning on coming or we haven't found you yet! go.bsky.app/6Vbwhjc
August 7, 2025 at 4:46 PM
Why not follow our @shigellameeting.bsky.social starterpack of people who are speaking at and attending the conference - please message to be added to the starter pack if you're planning on coming or we haven't found you yet! go.bsky.app/6Vbwhjc
Reposted by Malaka De Silva
I hope all my fellow #shigellaphiles have 20 - 24 April 2026 blocked out in their diaries for @shigellameeting.bsky.social next year in Paris! In the meantime, check out (and join) our starter pack to start community building now 🧫
Why not follow our @shigellameeting.bsky.social starterpack of people who are speaking at and attending the conference - please message to be added to the starter pack if you're planning on coming or we haven't found you yet! go.bsky.app/6Vbwhjc
August 7, 2025 at 4:49 PM
I hope all my fellow #shigellaphiles have 20 - 24 April 2026 blocked out in their diaries for @shigellameeting.bsky.social next year in Paris! In the meantime, check out (and join) our starter pack to start community building now 🧫
Reposted by Malaka De Silva
There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
August 1, 2025 at 6:29 PM
Reposted by Malaka De Silva
It was great fun writing this review with @gemccallum.bsky.social , even if our conclusions are rather scary. Lots of important pathogen evolution must be occurring outside of the infection context...
Delighted to have this review out with @jpjhall.bsky.social!
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens
doi.org
July 31, 2025 at 3:22 PM
It was great fun writing this review with @gemccallum.bsky.social , even if our conclusions are rather scary. Lots of important pathogen evolution must be occurring outside of the infection context...
Reposted by Malaka De Silva
Huge amount of work in this paper, very proud of Hugh getting through all these benchmarking tests. We’re much more confident now using ONT-only data for our clinical questions
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...
www.medrxiv.org/content/10.1...
July 30, 2025 at 8:34 AM
Huge amount of work in this paper, very proud of Hugh getting through all these benchmarking tests. We’re much more confident now using ONT-only data for our clinical questions
Reposted by Malaka De Silva
Delighted to have this review out with @jpjhall.bsky.social!
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens
doi.org
July 30, 2025 at 8:14 AM
Delighted to have this review out with @jpjhall.bsky.social!
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
Reposted by Malaka De Silva
There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
July 27, 2025 at 8:35 AM
There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n
Reposted by Malaka De Silva
Please share! 🦠
Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra.
Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/...
#MicroSky
Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra.
Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/...
#MicroSky
July 22, 2025 at 7:03 PM
Please share! 🦠
Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra.
Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/...
#MicroSky
Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra.
Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/...
#MicroSky
Reposted by Malaka De Silva
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 23, 2025 at 7:35 AM
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
Reposted by Malaka De Silva
@ksbakes.bsky.social is representing PDU at the GRC Microbial Population Biology conference this week introducing the AMR through time and space session - check out the work of the other attendees here:
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
July 6, 2025 at 9:41 PM
@ksbakes.bsky.social is representing PDU at the GRC Microbial Population Biology conference this week introducing the AMR through time and space session - check out the work of the other attendees here:
Reposted by Malaka De Silva
💫Don't miss the N&V💫
📰Organoid models advance dysentery control.
By Sydney L. Miles & Serge Mostowy.
⬇️
www.nature.com/articles/s41...
📰Organoid models advance dysentery control.
By Sydney L. Miles & Serge Mostowy.
⬇️
www.nature.com/articles/s41...
Organoid models advance dysentery control - Nature Genetics
Shigella is a major human pathogen with a stark lack of pipelines linking genome content to clinical pathogenesis. An innovative study using large-scale organoid models, combined with genome-wide muta...
www.nature.com
June 23, 2025 at 2:14 PM
💫Don't miss the N&V💫
📰Organoid models advance dysentery control.
By Sydney L. Miles & Serge Mostowy.
⬇️
www.nature.com/articles/s41...
📰Organoid models advance dysentery control.
By Sydney L. Miles & Serge Mostowy.
⬇️
www.nature.com/articles/s41...
Reposted by Malaka De Silva
Thank you to everyone who attended the 3rd UK MGE workshop. What an incredible few days of science and community building! Next stop: York 2026, hosted by @pcmfogg.bsky.social. See you all next year! #UKMGE
June 19, 2025 at 11:04 AM
Thank you to everyone who attended the 3rd UK MGE workshop. What an incredible few days of science and community building! Next stop: York 2026, hosted by @pcmfogg.bsky.social. See you all next year! #UKMGE
Reposted by Malaka De Silva
🚨 Reminder! You have just over two weeks to submit an abstract, if you want to present at the @microbiologysociety.org meeting "Understanding and predicting microbial evolutionary dynamics" in Liverpool in November! #microsky 🦠🧫🔬
‼️Update! Abstract submission is now open for the 2025 Liverpool UK @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics”! Deadline July 7th #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...
June 20, 2025 at 2:35 PM
🚨 Reminder! You have just over two weeks to submit an abstract, if you want to present at the @microbiologysociety.org meeting "Understanding and predicting microbial evolutionary dynamics" in Liverpool in November! #microsky 🦠🧫🔬