Ronan Doyle
@ronandoyle.bsky.social
Clinical bioinformatician at St Thomas' Hospital in London, UK (Synnovis).
Working on infectious disease diagnostics. Pathogen genomics and metagenomics.
Working on infectious disease diagnostics. Pathogen genomics and metagenomics.
Reposted by Ronan Doyle
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by Ronan Doyle
#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 Ronan Doyle
What an inspiring day! Last week we hosted our second Network Day, bringing together over 120 people. We explored the development of the national pilot metagenomic service, which is improving detection & treatment of respiratory infections. Thank you to all who joined and to our fantastic speakers!
November 13, 2025 at 4:53 PM
What an inspiring day! Last week we hosted our second Network Day, bringing together over 120 people. We explored the development of the national pilot metagenomic service, which is improving detection & treatment of respiratory infections. Thank you to all who joined and to our fantastic speakers!
Reposted by Ronan Doyle
Possibly one of the biggest changes in microbiology has been going on quietly over the past decade. Whilst this remains a diagnostic in development- and we have much to learn about how to use it- it represents a step change in how we manage infections.
New research article
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
November 7, 2025 at 2:35 PM
Possibly one of the biggest changes in microbiology has been going on quietly over the past decade. Whilst this remains a diagnostic in development- and we have much to learn about how to use it- it represents a step change in how we manage infections.
Reposted by Ronan Doyle
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)
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 Ronan Doyle
New research article
Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #AMR #WGS #OpenAccess #OA
Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #AMR #WGS #OpenAccess #OA
October 8, 2025 at 8:28 AM
New research article
Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #AMR #WGS #OpenAccess #OA
Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #AMR #WGS #OpenAccess #OA
Reposted by Ronan Doyle
New research article
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
October 2, 2025 at 8:47 AM
New research article
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
Reposted by Ronan Doyle
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co
academic.oup.com
April 22, 2025 at 5:00 AM
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...
Reposted by Ronan Doyle
🚨 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 1:03 PM
🚨 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...
Reposted by Ronan Doyle
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
July 22, 2025 at 9:59 PM
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Reposted by Ronan Doyle
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
Reposted by Ronan Doyle
1 hour lab-in-tube assay for TB!
"point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure"
www.science.org/doi/10.1126/...
"point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure"
www.science.org/doi/10.1126/...
Rapid tuberculosis diagnosis from respiratory or blood samples by a low cost, portable lab-in-tube assay
A low complexity, portable lab-in-tube tuberculosis assay for resource-limited areas analyzes blood, saliva, and sputum with a handheld device.
www.science.org
April 19, 2025 at 12:03 AM
1 hour lab-in-tube assay for TB!
"point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure"
www.science.org/doi/10.1126/...
"point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure"
www.science.org/doi/10.1126/...
Reposted by Ronan Doyle
"Importantly, the metagenomic tests provide results within 6–8 h"
That's quick!
#metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
That's quick!
#metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
UK launch metagenomic pathogen surveillance programme
On Jan 30, 2025, the UK Health Security Agency (UKHSA) announced the launch of the
metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE)—the world’s
first biosecurity surveillance sy...
www.thelancet.com
April 14, 2025 at 7:32 AM
"Importantly, the metagenomic tests provide results within 6–8 h"
That's quick!
#metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
That's quick!
#metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Reposted by Ronan Doyle
Next speaker was Luke Blagdon Snell with Same-day pan-microbial metagenomics for personalized therapy and pathogen surveillance on the intensive care unit: a single-centre prospective study (escmid.reg.key4events.com/AbstractList...).
Same-day pan-microbial metagenomics for personalised therapy and pathogen surveillance on the intensive care unit: a single-centre prospective study
escmid.reg.key4events.com
April 13, 2025 at 4:03 AM
Next speaker was Luke Blagdon Snell with Same-day pan-microbial metagenomics for personalized therapy and pathogen surveillance on the intensive care unit: a single-centre prospective study (escmid.reg.key4events.com/AbstractList...).
Reposted by Ronan Doyle
Robbie Hammond presented next with Implementing same-day respiratory metagenomic diagnostics in paediatric intensive care (escmid.reg.key4events.com/AbstractList...). Their method had a turnaround time of 6 hours.
Implementing same-day respiratory metagenomic diagnostics in paediatric intensive care
escmid.reg.key4events.com
April 13, 2025 at 4:03 AM
Robbie Hammond presented next with Implementing same-day respiratory metagenomic diagnostics in paediatric intensive care (escmid.reg.key4events.com/AbstractList...). Their method had a turnaround time of 6 hours.
Reposted by Ronan Doyle
Pan-microbial metagenomics protocol v1.2Public workspaceCritical
search.app
February 4, 2025 at 9:28 PM
Reposted by Ronan Doyle
Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...
Microbiome science needs more microbiologists - Nature Microbiology
Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.
www.nature.com
January 23, 2025 at 5:14 PM
Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...
Reposted by Ronan Doyle
Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
www.microbiologyresearch.org/content/jour...
(1/4)
www.microbiologyresearch.org/content/jour...
(1/4)
Exploring SNP filtering strategies: the influence of strict vs soft core
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...
www.microbiologyresearch.org
January 20, 2025 at 10:24 PM
Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
www.microbiologyresearch.org/content/jour...
(1/4)
www.microbiologyresearch.org/content/jour...
(1/4)
Reposted by Ronan Doyle
⚠️ BREAKING:
The suspected H5N1 bird flu infected child in Marin county drank raw milk, according to Marin HHS.
The child presented to a local emergency department with fever and vomiting. No other family members became sick, indicating no person-to-person transmission.
The suspected H5N1 bird flu infected child in Marin county drank raw milk, according to Marin HHS.
The child presented to a local emergency department with fever and vomiting. No other family members became sick, indicating no person-to-person transmission.
December 11, 2024 at 6:10 AM
⚠️ BREAKING:
The suspected H5N1 bird flu infected child in Marin county drank raw milk, according to Marin HHS.
The child presented to a local emergency department with fever and vomiting. No other family members became sick, indicating no person-to-person transmission.
The suspected H5N1 bird flu infected child in Marin county drank raw milk, according to Marin HHS.
The child presented to a local emergency department with fever and vomiting. No other family members became sick, indicating no person-to-person transmission.
Reposted by Ronan Doyle
@UKHSA latest respiratory surveillance released.
1.flu positivity and hospitalisations rising fast - earlier than last year and exponential growth
2. RSV remains high but looks like it is close to peak - highest rates in children under 5.
3. COVID at low levels and stable.
1.flu positivity and hospitalisations rising fast - earlier than last year and exponential growth
2. RSV remains high but looks like it is close to peak - highest rates in children under 5.
3. COVID at low levels and stable.
December 5, 2024 at 2:12 PM
@UKHSA latest respiratory surveillance released.
1.flu positivity and hospitalisations rising fast - earlier than last year and exponential growth
2. RSV remains high but looks like it is close to peak - highest rates in children under 5.
3. COVID at low levels and stable.
1.flu positivity and hospitalisations rising fast - earlier than last year and exponential growth
2. RSV remains high but looks like it is close to peak - highest rates in children under 5.
3. COVID at low levels and stable.
Reposted by Ronan Doyle
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
December 3, 2024 at 10:01 AM
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
Reposted by Ronan Doyle
It’s remarkable that the events of the 2019 Samoa measles outbreak aren’t more widely known: www.telegraph.co.uk/news/measles...
November 5, 2024 at 5:05 PM
It’s remarkable that the events of the 2019 Samoa measles outbreak aren’t more widely known: www.telegraph.co.uk/news/measles...
Reposted by Ronan Doyle
Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
November 13, 2024 at 5:15 PM
Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
Gonna need to get a round in
November 13, 2024 at 11:22 AM
Gonna need to get a round in