Marit Hetland

The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!

Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!

klebnet.org/2025/11/18/k...

New online! Microbial genomics for antimicrobial resistance ecology and action

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants BACKGROUND Ciprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. Whilst there are known K...

Come for the Klebs resistance data, stay for the DataViz! Massive congratulations to @karatsang.bsky.social on juggling such a huge meta-analysis; Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype, genotype, global resistance patterns #MicroSky 💻🧬 www.biorxiv.org/content/10.1...

Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social

Annual Norwegian NORM/NORM-VET report released.
Norway’s strict antibiotic policies pay off. Record-low use in humans & animals, and some of Europe’s lowest #AMR rates. But ESBL & VRE are on the rise, so vigilance is vital.

www.unn.no/4a675d/sitea...

Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches

Excited to share 9 fully funded PhD projects with NIHR HPRU Public Health genomics at UKHSA and University of Birmingham. Deadline 31 July www.birmingham.ac.uk/research/cen...
Ranging from methods development, microbiome, metagenomics and species specific (TB, Strep pneumo, measles) projects

Complete genomes of 568 diverse Klebsiella pneumoniae species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020 | Microbiology Resource Announcements Klebsiella pneumoniae species complex are opportunistic pathogens that can transmit between humans, animals, and the environment (1). Here, we report hybrid genome assemblies of 578 (568 complete) gen...

Happy to share this resource of 568 closed Klebsiella pneumoniae species complex hybrid assemblies, including 1416 plasmids! ⭕️🦠

We hope this will be useful
- short reads, long reads, hybrid assembly or all combined - for your own tools/validations 🥳 #Microsky

journals.asm.org/doi/10.1128/...

Invited & Abstract Programme Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).

There is still time to submit an abstract for #IMMEMXIV so don’t miss this chance and join us in Porto! Link for submission: www.escmid.org/congress-eve...

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

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...

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....

Fast and Accurate in silico Antigen Typing with Kaptive 3 Surface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide structures that are encoded by distinct biosynthesis gene clusters, e.g. the Klebsiella pneumoniae species complex (KpSC) K- and O- loci encode the synthesis machinery for the capsule (K) and outer-lipopolysaccharides (O), respectively. We previously presented Kaptive and Kaptive 2, programs to identify K and O-loci directly from KpSC genome assemblies (later adapted for Acinetobacter baumannii), enabling sero-epidemiological analyses to guide vaccine and phage therapy development. However, for some KpSC genome collections, Kaptive (v≤2) was unable to type a high proportion of K-loci. Here we identify the cause of this issue as assembly fragmentation, and present a new version of Kaptive (v3) to circumvent this problem, reduce processing times and simplify output interpretation. We compared the performance of Kaptive v2 and Kaptive v3 for typing genome assemblies generated from subsampled Illumina read sets (decrements of 10x depth), for which a corresponding high quality completed genome was also available to determine the 'true' loci (n=549 KpSC, n=198 A. baumannii). Both versions of Kaptive showed high rates of agreement to the matched true locus among 'typeable' locus calls (≥96% for ≥20x read depth), but Kaptive v3 was more sensitive, particularly for low depth assemblies (at <40x depth, v3 ranged 0.85-1 vs v2 0.09-0.94) and/or typing KpSC K-loci (e.g. 0.97 vs 0.82 for non-subsampled assemblies). Overall, Kaptive v3 was also associated with a higher rate of optimal outcomes i.e. loci matching those in the reference database were correctly typed and genuine novel loci were reported as untypeable (73-98% for v3 vs 7-77% for v2 for KpSC K-loci). Kaptive v3 was >1 order of magnitude faster than Kaptive v2 making it easy to analyse thousands of assemblies on a desktop computer, facilitating broadly accessible in silico serotyping that is both accurate and sensitive. The Kaptive v3 source code is freely available on GitHub (https://github.com/klebgenomics/Kaptive), and has been implemented in Kaptive Web (https://kaptive-web.erc.monash.edu). ### Competing Interest Statement The authors have declared no competing interest.

Super excited to finally present the preprint to accompany Kaptive 3 which we released last year!

Big thanks to coauthors @kelwyres.bsky.social, @katholt.bsky.social, @genomarit.bsky.social and Iren Löhr.

Here's what we did to improve in silico antigen typing 👇🧵
www.biorxiv.org/content/10.1...

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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National One Health Strategy Against Antimicrobial Resistance 2024–2033 Antimicrobial resistance (AMR) is one of the most pressing health challenges in the world. Without effective measures, this problem will only intensify for future generations. Efforts to combat AMR ar...

The Norwegian One Health Strategy Against AMR 2024–2033 is now available in English. It emphasizes a cross-sectoral approach and global cooperation to reduce infections and preserve effective antimicrobial agents.

www.regjeringen.no/en/dokumente...

Please add me

A small history lesson in #Klebsiella genomics in honour of #KLEBS24…
2009 was a big year for Klebs!
- First genome published
- First description of ST258 KPC-producing clone
pubmed.ncbi.nlm.nih.gov/19218573/
- First description of NDM-1 beta-lactamase
pubmed.ncbi.nlm.nih.gov/19770275/

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs 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 clinical relev...

Interesting One Health study on Klebsiella pneumonie in Norway, which seems to confirm that there is little (but not no) spillover between human and non-human niches

www.biorxiv.org/content/10.1...

Presented by Marit Hetland #Klebsiella2024

Our study highlights the importance of infection prevention in human clinical settings. However, reducing transmission that leads to colonisation - e.g. from direct contact with animals or via the food chain - could also play an important role in reducing the KpSC disease burden 🦠

While most KpSC infections in humans were linked to human isolates, we found ~5% had close relatives in animal and marine environments, despite being separated by time and location

The KpSc populations were distinct but overlapped across human, animal and marine sources, however there were few recent transmission events across the niches

Excited to share this preprint where we’ve used genomic analysis of >3000 genomes to study Klebsiella pneumoniae in a One Health perspective 🦠🔬👩‍💻 #OneHealth #KLEBGAP #KlebClub #IrenLöhr @katholt.bsky.social #NORKLEBNET

PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students.
#microsky
www.findaphd.com/phds/project...