Ewan Harrison
@ewanharrison.bsky.social
Microbiologist at the Wellcome Sanger Institute and University of Cambridge.
Reposted by Ewan Harrison
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
Reposted by Ewan Harrison
ICYMI: New online! Unpacking the spread of pathogens
Unpacking the spread of pathogens
Nature Reviews Microbiology, Published online: 17 November 2025; doi:10.1038/s41579-025-01264-wThis Genome Watch discusses recent advances in genomic epidemiology that enable the reconstruction of transmission events, with greater resolution and across more complex settings at scale.
www.nature.com
November 24, 2025 at 9:25 PM
ICYMI: New online! Unpacking the spread of pathogens
Reposted by Ewan Harrison
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Benchmarking of human read removal strategies for viral and microbial metagenomics
Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological a…
www.sciencedirect.com
November 6, 2025 at 4:19 PM
Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...
Reposted by Ewan Harrison
featuring @duncan-ng.bsky.social @pathogenomenick.bsky.social @emmanuel-saliba.bsky.social @resp-micro.bsky.social @asthmaandlung.org.uk @ewanharrison.bsky.social @ryanthwaites.bsky.social and many many more I can't find on bluesky
October 8, 2025 at 2:56 PM
featuring @duncan-ng.bsky.social @pathogenomenick.bsky.social @emmanuel-saliba.bsky.social @resp-micro.bsky.social @asthmaandlung.org.uk @ewanharrison.bsky.social @ryanthwaites.bsky.social and many many more I can't find on bluesky
Reposted by Ewan Harrison
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211
Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.
coursesandconferences.wellcomeconnectingscience.org
October 8, 2025 at 2:48 PM
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Reposted by Ewan Harrison
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 Ewan Harrison
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...
🧵 (1/14)
www.doi.org/10.1038/s414...
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 ...
www.doi.org
July 17, 2025 at 12:13 PM
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...
🧵 (1/14)
www.doi.org/10.1038/s414...
Reposted by Ewan Harrison
More of this kind of thing.
July 11, 2025 at 7:39 AM
More of this kind of thing.
Reposted by Ewan Harrison
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
May 22, 2025 at 4:06 PM
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
Happy to share our first preprint looking at the nasal microbiome in ~1000 healthy adults from the CARRIAGE study of 20,000 healthy blood donors to understand nasal colonisation by Staphylococcus aureus. Ten years in the making! doi.org/10.21203/rs....
The nasal microbiome redefines Staphylococcus aureus colonisation
Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large ...
doi.org
May 7, 2025 at 11:35 AM
Happy to share our first preprint looking at the nasal microbiome in ~1000 healthy adults from the CARRIAGE study of 20,000 healthy blood donors to understand nasal colonisation by Staphylococcus aureus. Ten years in the making! doi.org/10.21203/rs....
Reposted by Ewan Harrison
Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa
Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but...
www.biorxiv.org
May 1, 2025 at 6:32 AM
Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ewan Harrison
If you can't afford to use a diagnostic test, then its relative performance characteristics become irrelevant.
Important issue raised re blood cultures 👇 @lancetmicrobe.bsky.social
#ClinMicro #IDSky #AMR
www.thelancet.com/journals/lan...
Important issue raised re blood cultures 👇 @lancetmicrobe.bsky.social
#ClinMicro #IDSky #AMR
www.thelancet.com/journals/lan...
The cost of blood cultures: a barrier to diagnosis in low-income and middle-income countries
The recent Editorial by The Lancet Microbe, titled Rethinking blood culture, highlights
the blood culture bottle shortage in the USA and the overreliance on single manufacturers.1
The shortages of blo...
www.thelancet.com
March 31, 2025 at 7:32 AM
If you can't afford to use a diagnostic test, then its relative performance characteristics become irrelevant.
Important issue raised re blood cultures 👇 @lancetmicrobe.bsky.social
#ClinMicro #IDSky #AMR
www.thelancet.com/journals/lan...
Important issue raised re blood cultures 👇 @lancetmicrobe.bsky.social
#ClinMicro #IDSky #AMR
www.thelancet.com/journals/lan...
Reposted by Ewan Harrison
There were more than 125,000 measles cases in the WHO European region in 2024 - the highest number since 1997!
38 deaths have been reported so far, every single one of them preventable.
Worth remembering this also as we report on the measles outbreak in the US.
🧪 #IDsky
38 deaths have been reported so far, every single one of them preventable.
Worth remembering this also as we report on the measles outbreak in the US.
🧪 #IDsky
March 13, 2025 at 12:02 PM
There were more than 125,000 measles cases in the WHO European region in 2024 - the highest number since 1997!
38 deaths have been reported so far, every single one of them preventable.
Worth remembering this also as we report on the measles outbreak in the US.
🧪 #IDsky
38 deaths have been reported so far, every single one of them preventable.
Worth remembering this also as we report on the measles outbreak in the US.
🧪 #IDsky
Reposted by Ewan Harrison
Weeks ago I highlighted the false balance of “if only scientists could communicate better”.
One OpEd writer kindly reached out to me and I want to share my main response to them because I find it remarkable that people still can’t see what we are now all seeing has been under way for years.
🧵👇
One OpEd writer kindly reached out to me and I want to share my main response to them because I find it remarkable that people still can’t see what we are now all seeing has been under way for years.
🧵👇
February 9, 2025 at 9:32 PM
Weeks ago I highlighted the false balance of “if only scientists could communicate better”.
One OpEd writer kindly reached out to me and I want to share my main response to them because I find it remarkable that people still can’t see what we are now all seeing has been under way for years.
🧵👇
One OpEd writer kindly reached out to me and I want to share my main response to them because I find it remarkable that people still can’t see what we are now all seeing has been under way for years.
🧵👇
Reposted by Ewan Harrison
Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms
rdcu.be/d55l3
rdcu.be/d55l3
The mutational landscape of Staphylococcus aureus during colonisation
Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...
rdcu.be
January 14, 2025 at 9:40 AM
Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms
rdcu.be/d55l3
rdcu.be/d55l3
Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3
@fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social
@fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social
The mutational landscape of Staphylococcus aureus during colonisation
Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...
rdcu.be
January 13, 2025 at 1:06 PM
Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3
@fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social
@fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social
Reposted by Ewan Harrison
Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2
1/n
1/n
December 19, 2024 at 8:48 PM
Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2
1/n
1/n
Reposted by Ewan Harrison
Frustrating - I reviewed a paper that was highly problematic, mainly in scientific rigour undermining most of the conclusions, so I recommend Reject. However the editor decides to Revise presumably due to the more positive comments from reviewer 2... /1
December 11, 2024 at 9:09 AM
Frustrating - I reviewed a paper that was highly problematic, mainly in scientific rigour undermining most of the conclusions, so I recommend Reject. However the editor decides to Revise presumably due to the more positive comments from reviewer 2... /1
Reposted by Ewan Harrison
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
December 9, 2024 at 7:15 PM
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Reposted by Ewan Harrison
UK PhD stipends have not been increasing in line with the national minimum wage, and since the generous COVID increase haven’t even bothered to be anchored against an inflation metric. I’m lucky enough to have a spouse to support me but in what world is this not a barrier to entry for others?
December 1, 2024 at 7:56 AM
UK PhD stipends have not been increasing in line with the national minimum wage, and since the generous COVID increase haven’t even bothered to be anchored against an inflation metric. I’m lucky enough to have a spouse to support me but in what world is this not a barrier to entry for others?
Reposted by Ewan Harrison
Applied Bioinformatics & Public Health Microbiology (21-23 May 2025) is open for registrations!
Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social
@ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social
Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social
@ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social
Bluesky
anharrison.bsky.social
November 29, 2024 at 5:12 PM
Applied Bioinformatics & Public Health Microbiology (21-23 May 2025) is open for registrations!
Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social
@ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social
Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social
@ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social
Reposted by Ewan Harrison
last couple days to apply (for free! from anywhere in the world!) to the Sanger 2025 PhD Programme — Deadline: 28th November 2024 (09:00 GMT)
For more info, visit www.sanger.ac.uk/about/study/...
For more info, visit www.sanger.ac.uk/about/study/...
November 25, 2024 at 6:34 PM
last couple days to apply (for free! from anywhere in the world!) to the Sanger 2025 PhD Programme — Deadline: 28th November 2024 (09:00 GMT)
For more info, visit www.sanger.ac.uk/about/study/...
For more info, visit www.sanger.ac.uk/about/study/...
Reposted by Ewan Harrison
First @bsky.app post! Great session today #FISHIS about the importance of learning from the pandemic for the future. Thanks @hisinfection.bsky.social @marionkoopmans.bsky.social @ewanharrison.bsky.social
November 22, 2024 at 10:37 PM
First @bsky.app post! Great session today #FISHIS about the importance of learning from the pandemic for the future. Thanks @hisinfection.bsky.social @marionkoopmans.bsky.social @ewanharrison.bsky.social
Reposted by Ewan Harrison
Antimicrobial resistance is rapidly rising in Shigella species. How up to date is your treatment guidance? Be sure to read our latest @LancetMicrobe comment to inform your thinking bit.ly/3Z6yNRa 1/10
Using demographics of patients to inform treatment of shigellosis in England
Shigellosis, caused by bacteria of the genus Shigella, is a diarrhoeal disease transmitted
by the faecal–oral route.1 Rapid increases in the prevalence of extensively drug-resistant
(XDR) Shigella iso...
bit.ly
November 15, 2024 at 8:25 PM
Antimicrobial resistance is rapidly rising in Shigella species. How up to date is your treatment guidance? Be sure to read our latest @LancetMicrobe comment to inform your thinking bit.ly/3Z6yNRa 1/10