Invasive meningococcal disease (IMD) remains a major global health threat. Despite vaccination, meningococcal genetic diversity means disease, includi…

A single mom, her two daughters, and the chatbots that fill in the gaps.

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...

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EMBO Workshop Shigella: from biology to prevention

Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...

Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

A new major version of ggplot2 has been released on CRAN. Find out what is new here.

Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, t...

An investigation of the European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) detected the same mosaic IncHI1B(pNDM-MAR) resistance (OXA-48) and virulence (aerobactin) plasmid in 4...

The pro-Israel lobby isn’t designed to balance debate nor to enrich it – it is designed to silence it.

Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...