Rasmus Marvig
@marvig.bsky.social
Computational biologist specialising in infectious disease genomics
Reposted by Rasmus Marvig
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
November 30, 2025 at 7:51 PM
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Reposted by Rasmus Marvig
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 Rasmus Marvig
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV
Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...
www.biorxiv.org
September 29, 2025 at 7:45 PM
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Reposted by Rasmus Marvig
The 2024 rankings of bacterial threats
August 27, 2025 at 4:19 PM
The 2024 rankings of bacterial threats
Reposted by Rasmus Marvig
How likely are SNP-based phenotypic reversions during human infection/coloniziation?
Our latest paper on the rare CF pathogen B. dolosa -- a great collaboration with folks I've worked with since my PhD and led by Alex Poret -- adds to the evidence that reversions are likely in large populations.
Our latest paper on the rare CF pathogen B. dolosa -- a great collaboration with folks I've worked with since my PhD and led by Alex Poret -- adds to the evidence that reversions are likely in large populations.
De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen - Nature Communications
Bacteria evolving within humans employ strategies to overcome trade-offs. Here, the authors report that the cystic fibrosis-associated pathogen Burkholderia dolosa alternates phenotypes in vivo by acc...
www.nature.com
July 23, 2025 at 4:35 PM
How likely are SNP-based phenotypic reversions during human infection/coloniziation?
Our latest paper on the rare CF pathogen B. dolosa -- a great collaboration with folks I've worked with since my PhD and led by Alex Poret -- adds to the evidence that reversions are likely in large populations.
Our latest paper on the rare CF pathogen B. dolosa -- a great collaboration with folks I've worked with since my PhD and led by Alex Poret -- adds to the evidence that reversions are likely in large populations.
Reposted by Rasmus Marvig
New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs.
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
July 3, 2025 at 6:52 PM
New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs.
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Reposted by Rasmus Marvig
1/8 - New in @natcomms.nature.com !
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
In-host evolution of Yersinia enterocolitica during a chronic human infection - Nature Communications
This study documents the evolution of antibiotic resistance and major growth defects in Yersinia enterocolitica in a patient over 14 years, revealing genetic changes that shed light on bacterial adapt...
www.nature.com
July 1, 2025 at 6:05 PM
1/8 - New in @natcomms.nature.com !
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
Reposted by Rasmus Marvig
TreeHub: a comprehensive dataset of phylogenetic trees www.nature.com/articles/s41... 🧬🖥️🧪 github.com/wpwupingwp/t...
June 11, 2025 at 8:01 PM
TreeHub: a comprehensive dataset of phylogenetic trees www.nature.com/articles/s41... 🧬🖥️🧪 github.com/wpwupingwp/t...
Reposted by Rasmus Marvig
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 9:35 AM
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
Reposted by Rasmus Marvig
Today "a milestone in the evolution of personalized therapies for rare & ultra-rare inborn errors of metabolism"
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
May 15, 2025 at 6:05 PM
Today "a milestone in the evolution of personalized therapies for rare & ultra-rare inborn errors of metabolism"
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
—the 1st human to undergo custom genome editing
—from decades of NIH funded research
www.nejm.org/doi/full/10....
@nejm.org
www.nejm.org/doi/full/10....
www.nytimes.com/2025/05/15/h...
Reposted by Rasmus Marvig
Great paper by @target-amr.bsky.social leadership team colleagues @drtessjohnson.bsky.social and Steph Johnson on the ethics of clinical metagenomics
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Clinical metagenomics: ethical issues
Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or foll...
www.microbiologyresearch.org
May 9, 2025 at 8:35 AM
Great paper by @target-amr.bsky.social leadership team colleagues @drtessjohnson.bsky.social and Steph Johnson on the ethics of clinical metagenomics
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Rasmus Marvig
Great paper out by Ben Chan, Jon Koff and co at Yale highlighting compassionate use of phage therapy in nine patients with CF with multi-drug resistant strains of Pseudomonas aeruginosa
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis - Nature Medicine
A novel personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off may represent a viable alternative approach for the treatment of antimicrobial-resistant bacteria...
www.nature.com
May 1, 2025 at 2:29 PM
Great paper out by Ben Chan, Jon Koff and co at Yale highlighting compassionate use of phage therapy in nine patients with CF with multi-drug resistant strains of Pseudomonas aeruginosa
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rasmus Marvig
Human de novo mutation rates from a four-generation pedigree reference www.nature.com/articles/s41... 🧬🖥️🧪
May 2, 2025 at 6:30 PM
Human de novo mutation rates from a four-generation pedigree reference www.nature.com/articles/s41... 🧬🖥️🧪
Reposted by Rasmus Marvig
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
Reposted by Rasmus Marvig
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 Rasmus Marvig
Our paper out in @cidjournal.bsky.social
2-years of real-time genomic surveillance + intervention
- 172 outbreaks, 476 transmissions
- 95% of interventions halted transmission
- 62 infxs prevented
- $695,000 net savings, 3.2 ROI
Should this be standard? #IDSky
📄: academic.oup.com/cid/advance-...
2-years of real-time genomic surveillance + intervention
- 172 outbreaks, 476 transmissions
- 95% of interventions halted transmission
- 62 infxs prevented
- $695,000 net savings, 3.2 ROI
Should this be standard? #IDSky
📄: academic.oup.com/cid/advance-...
April 30, 2025 at 11:35 AM
Our paper out in @cidjournal.bsky.social
2-years of real-time genomic surveillance + intervention
- 172 outbreaks, 476 transmissions
- 95% of interventions halted transmission
- 62 infxs prevented
- $695,000 net savings, 3.2 ROI
Should this be standard? #IDSky
📄: academic.oup.com/cid/advance-...
2-years of real-time genomic surveillance + intervention
- 172 outbreaks, 476 transmissions
- 95% of interventions halted transmission
- 62 infxs prevented
- $695,000 net savings, 3.2 ROI
Should this be standard? #IDSky
📄: academic.oup.com/cid/advance-...
Reposted by Rasmus Marvig
I love both these stories. They are inspiring, and I am also working heavily on metagenomic diagnostics
But this also shows we have made little to zero progress in a decade in using NGS in clinical microbiology and ID, which is depressing
www.bbc.co.uk/news/article...
www.nejm.org/doi/10.1056/...
But this also shows we have made little to zero progress in a decade in using NGS in clinical microbiology and ID, which is depressing
www.bbc.co.uk/news/article...
www.nejm.org/doi/10.1056/...
April 30, 2025 at 12:19 PM
I love both these stories. They are inspiring, and I am also working heavily on metagenomic diagnostics
But this also shows we have made little to zero progress in a decade in using NGS in clinical microbiology and ID, which is depressing
www.bbc.co.uk/news/article...
www.nejm.org/doi/10.1056/...
But this also shows we have made little to zero progress in a decade in using NGS in clinical microbiology and ID, which is depressing
www.bbc.co.uk/news/article...
www.nejm.org/doi/10.1056/...
Reposted by Rasmus Marvig
🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs - Genome Medicine
Background Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the cli...
genomemedicine.biomedcentral.com
April 30, 2025 at 9:33 AM
🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
Reposted by Rasmus Marvig
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
www.biorxiv.org
April 28, 2025 at 8:08 AM
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Reposted by Rasmus Marvig
Antibiotics are life-saving, but even short use can drive resistance in gut bacteria, with mutations lasting over a year, as seen here for ciprofloxacin.
Antibiotic stewardship helps protect these powerful drugs for the future.
#AMR #OneHealth #AntibioticResistance
www.nature.com/articles/s41...
Antibiotic stewardship helps protect these powerful drugs for the future.
#AMR #OneHealth #AntibioticResistance
www.nature.com/articles/s41...
Brief antibiotic use drives human gut bacteria towards low-cost resistance - Nature
Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...
www.nature.com
April 23, 2025 at 6:54 PM
Antibiotics are life-saving, but even short use can drive resistance in gut bacteria, with mutations lasting over a year, as seen here for ciprofloxacin.
Antibiotic stewardship helps protect these powerful drugs for the future.
#AMR #OneHealth #AntibioticResistance
www.nature.com/articles/s41...
Antibiotic stewardship helps protect these powerful drugs for the future.
#AMR #OneHealth #AntibioticResistance
www.nature.com/articles/s41...
Reposted by Rasmus Marvig
I spent a week in Georgia 🇬🇪 talking about genomic epidemiology: from the very basics to case studies and false information as a part of the EU funded TWINNING project. It was a week full of beautiful Tbilisi 🏔, incredible food 🥘 and insightful discussions about the power of genomic epidemiology 🧬.
April 14, 2025 at 8:57 AM
I spent a week in Georgia 🇬🇪 talking about genomic epidemiology: from the very basics to case studies and false information as a part of the EU funded TWINNING project. It was a week full of beautiful Tbilisi 🏔, incredible food 🥘 and insightful discussions about the power of genomic epidemiology 🧬.
Reposted by Rasmus Marvig
Ceftazidime-avibactam (a last resort drug) use selects multidrug-resistance and prevents designing collateral sensitivity based therapies against P. aeruginosa (no robust patterns emerge). Happy to see it published! 🥳 @cnb-csic.bsky.social @idisba.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Ceftazidime-avibactam use selects multidrug-resistance and prevents designing collateral sensitivity-based therapies against Pseudomonas aeruginosa - Nature Communications
Ceftazidime-avibactam is a β-lactam/β-lactamase inhibitor combination restricted for the treatment of multidrug-resistant infections of Pseudomonas aeruginosa non-susceptible to ceftazidime and resist...
www.nature.com
April 9, 2025 at 9:47 AM
Ceftazidime-avibactam (a last resort drug) use selects multidrug-resistance and prevents designing collateral sensitivity based therapies against P. aeruginosa (no robust patterns emerge). Happy to see it published! 🥳 @cnb-csic.bsky.social @idisba.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rasmus Marvig
Dear American friends.
We agree that status quo in the Artcic is not an option.
So let’s talk about how we can fix it - together.
Lars Løkke Rasmussen
Danish Foreign Minister
We agree that status quo in the Artcic is not an option.
So let’s talk about how we can fix it - together.
Lars Løkke Rasmussen
Danish Foreign Minister
March 28, 2025 at 11:42 PM
Dear American friends.
We agree that status quo in the Artcic is not an option.
So let’s talk about how we can fix it - together.
Lars Løkke Rasmussen
Danish Foreign Minister
We agree that status quo in the Artcic is not an option.
So let’s talk about how we can fix it - together.
Lars Løkke Rasmussen
Danish Foreign Minister
Reposted by Rasmus Marvig
Cell free microbial DNA as a biomarker of Infection is nascent, but intriguing.
Intuitively it makes sense, but undoubtedly we'll end up in the weeds of sensitivity, specificity and defining the true gold standard for clearance of infection!
#IDSky #ClinMicro #AMR
@cidjournal.bsky.social
Intuitively it makes sense, but undoubtedly we'll end up in the weeds of sensitivity, specificity and defining the true gold standard for clearance of infection!
#IDSky #ClinMicro #AMR
@cidjournal.bsky.social
Quantitative Microbial Cell-Free DNA Sequencing from Plasma: A Potential Biomarker for the Diagnosis of Staphylococcal Infection of Cardiac Implantable Electronic Devices
Among patients with cardiac implantable electronic devices experiencing staphylococcal bacteremia, quantitative microbial cell-free DNA detected in plasma
academic.oup.com
March 14, 2025 at 7:11 PM
Cell free microbial DNA as a biomarker of Infection is nascent, but intriguing.
Intuitively it makes sense, but undoubtedly we'll end up in the weeds of sensitivity, specificity and defining the true gold standard for clearance of infection!
#IDSky #ClinMicro #AMR
@cidjournal.bsky.social
Intuitively it makes sense, but undoubtedly we'll end up in the weeds of sensitivity, specificity and defining the true gold standard for clearance of infection!
#IDSky #ClinMicro #AMR
@cidjournal.bsky.social
Reposted by Rasmus Marvig
Landmark paper claxon!
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
February 18, 2025 at 9:27 AM
Landmark paper claxon!
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.