Genome annotation is an important step in deriving functional meaning from prokaryotic sequencing data, yet systematic evaluations guiding tool selection are lacking. We present the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes. This includes Escherichia coli strains for baseline performance, thousands of archaea and bacteria genomes, as well as frameshifted and metagenome-assembled genomes. Bakta excels in annotating high-quality bacterial genomes, while PGAP was better for archaeal genomes and challenging bacterial assemblies, including metagenome-assembled, fragmented, or contaminated samples. For Gene Ontology annotation, PGAP consistently provides broader term coverage, whereas EggNOG-mapper offers more terms per feature. Our findings highlight tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin (e.g. MAGs). This study provides an evidence-based guide for users and informs future tool development.
Mateusz Jundzill, Martin Hölzer, S. Mangul et al.· Genome Biology· 0 citations
Hypervirulent community-associated MRSA clones such as Staphylococcus aureus (S. aureus) USA300 drive rapidly progressive necrotizing pneumonia with high morbidity and limited therapeutic options. Bacteriophage K (phage K) is a well-characterized lytic phage active against S. aureus, but its efficacy is limited by restricted host range and the emergence of bacterial resistance. Here, we subjected phage K to experimental evolution on S. aureus USA300 to select an adapted variant with enhanced bactericidal properties. Wild-type phage K and the evolved derivative, designated phage KJ25, were compared using growth inhibition assays, time-kill kinetics, genomic differences and transcriptomic analyses of the bacterial response to infection. Efficacy was evaluated in an in vitro A549 lung epithelial cell infection model and ex vivo murine precision-cut lung slices (PCLS).Phage KJ25 exhibited significantly improved killing of USA300, achieving faster bacterial reduction and sustained suppression of regrowth. Genomic analysis identified a function-impairing mutation in gene gp102, encoding a predicted DNA-binding protein implicated in transcriptional regulation. RNA sequencing revealed that KJ25 infection of USA300 induced a slower and less disruptive host transcriptional takeover than wild-type phage K. Importantly, in both A549 cells and PCLS model, phage KJ25 markedly reduced bacterial burden while preserving lung tissue integrity, supporting its therapeutic potential.Collectively, these findings highlight the value of experimental evolution for tailoring therapeutic phages and support phage adaptation as a promising strategy for developing interventions against multidrug-resistant S. aureus.
Swanti Schapp, P. Seibold, Yasmina Reisser et al.· Emerging Microbes and Infect...· 0 citations
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