VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis In this phase 1 randomized trial of women with bacterial vaginosis in South Africa and the United States, Potloane et al. show that a multi-strain vaginal Lactobacillus crispatus live biotherapeutic administered for just 3–7 days following antibiotics can achieve vaginal colonization lasting up to 12 weeks.

#NatMicroPicks

Live biotherapeutics for bacterial vaginosis 🚺🦠

A short course of vaginal Lactobacillus crispatus biotherapeutics after antibiotics safely achieved sustained colonization in many women recovering from bacterial vaginosis.

#MicroSky

www.cell.com/cell-host-mi...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years

www.sciencedirect.com/science/arti...

🧪 This bacterial strain has been maintained in sterile water since 1994.

Possible carbon sources incl. “phthalic acid - a plastic degradation product likely leached from inoculation tubes“.

Genomic variations accumulated between 1994 and 2022 suggested adaptations to long-term nutrient deprivation

As no reflection at all on the excellent organisers or the excellence of this meeting. There is not a force in nature that would make me travel to the USA for a scientific meeting right now.

The genetic architecture of HIV-1 virulence Abstract. The virulence of HIV-1 is partly determined by viral genetic variation. Finding individual genetic variants affecting virulence is important for

François Blanquart et al. dive into the genetic basis of HIV virulence with very cool statistical methods. They show that viral load is shaped by host-dependent HLA escape variants with large effects, alongside many additional variants whose effects are too subtle to reach genome-wide significance.

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...

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 👇

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...

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...

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...

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...

The 2024 rankings of bacterial threats

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...

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.

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/...

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...

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...

TreeHub: a comprehensive dataset of phylogenetic trees www.nature.com/articles/s41... 🧬🖥️🧪 github.com/wpwupingwp/t...

I get "0 hits matched a rule " both when I tried on AMRrules/tests/data/input/test_ecoli_genome.tsv and 100 local P. aeruginosa genomes. · Issue #4 · interpretAMR/AMRrules Dear authors of AMRrules, Thanks for a promising tool. I get "0 hits matched a rule " both when I tried on AMRrules/tests/data/input/test_ecoli_genome.tsv and 100 local P. aeruginosa genomes. So I ...

Yep.
The test command/dataset works now. So I am one step further :)
I have created an issue: github.com/interpretAMR...
Thanks and sure that I will work for me and be a success for many.

Thanks for reply.
My old files were generated without --print_node option so I generated new files.
I tried on 100 P. aeruginosa and gets "0 hits matched a rule" for all. Same for test_ecoli_genome.tsv so it must be problem at my end. I may create an issue at github to get onwards from here.

Great work.
Does it take amrfinderplus v3 results as input or only newest armfinderplus v4 ?

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules

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...

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...

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...

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...

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...

Human de novo mutation rates from a four-generation pedigree reference www.nature.com/articles/s41... 🧬🖥️🧪

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]

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...

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...

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-...

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/...

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...

🦠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....

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...

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 🧵

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...

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...

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 🧬.

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...

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...