Wyres lab

Bacterial population genomics and metabolism

Publications

For a full list of publications visit GoogleScholar. Recent highlights are listed below.

  • Thomas D. Stanton, Shaun P. Keegan, [plus 78 others], Kelly L. Wyres and Kathryn E. Holt. 2025. Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage. medRxiv. doi: 10.1101/2025.06.28.25330253.
  • Thomas D. Stanton, Marit A.K. Hetland, Iren H. Löhr, Kathryn E. Holt, Kelly L. Wyres. 2025. Fast and accurate in silico antigen typing with Kaptive 3. Microbial Genomics. 11(6): doi: 10.1099/mgen.0.001428.
  • Chris Whitfield, Steven D. Kelly, Tom D. Stanton, Kelly L. Wyres, Bradley R. Clarke, Taylor J.B. Forrester, Agnieszka Kowalczyk. 2025. O-antigen polysaccharides in Klebsiella pneumoniae: structures and molecular basis for antigenic diversity. Microbiology and Molecular Biology Reviews. 21:e0009023. For free access to the full text accepted version click here.
  • Ben Vezina, Helena B. Cooper, Martin Rethoret-Pasty, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres. 2024. A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports persistent co-existence of diverse lineages. bioRxiv doi: https://doi.org/10.1101/2024.07.24.605038
  • HelenaB. Cooper, Ben Vezina, Jane Hawkey, Virginie Passet, Sebastián López-Fernández, Jonathan M. Monk, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres. 2024. A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. Microbial Genomics doi: https://doi.org/10.1099/mgen.0.001206
  • Ben Vezina, Stephen C. Watts, Jane Hawkey, Helena B. Cooper, Louise M. Judd, Adam Jenney, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres. 2023. Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models. eLife doi: https://doi.org/10.7554/eLife.87406.3
  • Jane Hawkey, Ben Vezina, Jonathan M. Monk, Louise M. Judd, Taylor Harshegyi, Sebastien Lopez-Fernandez, Carla Rodrigues C, Sylvain Brisse, Katheyn E. Holt and Kelly L. Wyres. 2022. A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome Research 32 1004-1014 doi: https://doi.org/10.1101/gr.276289.121.
  • Margaret M.C. Lam, Ryan R. Wick, Kathryn E. Holt and Kelly L Wyres. 2022. Kaptive 2.0: Updated capsule and LPS locus typing from Klebsiella whole genome sequences. Microbial Genomics 8:3 doi: https://doi.org/10.1099/mgen.0.000800.
  • Margaret M.C. Lam, Ryan R. Wick, Stephen C. Watts, Louise T. Cerdeira, Kelly L. Wyres and Kathryn E. Holt. 2021. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications 12: 4188 doi: https://doi.org/10.1038/s41467-021-24448-3.
  • Kelly L. Wyres, Margaret M.C. Lam and Kathryn E. Holt. 2020. Population genomics of Klebsiella pneumoniae. Nature Reviews Microbiology doi: https://doi.org/10.1038/s41579-019-0315-1.