The natural diversity of E. coli transporter-dependent capsules
Roese Mores, C.; Miravet-Verde, S.; Cacace, E.; Rutschmann, C.; Lin, C.-W.; Ruscheweyh, H. J.; Cuenod, A.; Cappio Barazzone, E.; Marrec, E.; Vershynina, K.; Schumann, R.; Bower, D. J.; Schubert, M.; Egli, A.; Fiebig, T.; Slack, E.; Sunagawa, S.; Keys, T. G.
Show abstract
Serotyping of bacteria using genomic information (in silico serotyping) has increasingly replaced serology. However, the E. coli capsule serotyping system has been largely abandoned since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution, and epidemiology. To address this, we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed >37,000 E. coli genomes, cataloging 85 transporter-dependent capsule types (K-types), including 55 novel ones. We leveraged this catalog to develop an in silico serotyping tool, kTYPr, and applied it to curated sets of >25,000 E. coli genomes and metagenome-assembled genomes spanning diverse environmental and clinical sources. We found novel K-types enriched in under-sampled environments and associated with E. coli disease. This research expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Antibiotic hypersensitivity signatures identify targets for attack in the Acinetobacter baumannii cell envelope 96%
- Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile 95%
- Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes 95%
Similar papers in this journal
- A bacterial pan-genome makes gene essentiality strain-dependent and evolvable 96%
- Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota 96%
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models 96%
Similar papers in this journal
- Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter 96%
- Computational exploration of the global microbiome for antibiotic discovery 95%
- Chimeric infective particles expand species boundaries in phage inducible chromosomal island mobilization 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.