Wyres lab

Bacterial population genomics and metabolism

Publications

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

  1. Thomas D. Stanton, Shaun P. Keegan, [plus 78 others], Kelly L. Wyres and Kathryn E. Holt. 2026. 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. PLoS Medicine doi: https://doi.org/10.1371/journal.pmed.1004879. Read the summary here.
  2. Ben Vezina, Helena B. Cooper, Christopher K. Barlow, Martin Rethoret-Pasty, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres. 2025. A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports persistent co-existence of diverse lineages. PLoS Biology doi: https://doi.org/10.1371/journal.pbio.3003559. Read the summary here.
  3. 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.
  4. 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.
  5. Helena B. 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
  6. 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
  7. 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.
  8. 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.
  9. 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.
  10. 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.