Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock: Evolutionary history of bovine Staphylococcus aureus

Gonzalo Yebra, Josh Harling-Lee, Samantha Lycett, Frank M. Aarestrup, Gunhild Larsen, Lina M. Cavaco, Keun Seok Seo, Sam Abraham, Jacqueline M. Norris, Tracy Schmid, Marthie M Ehlers, Daniel O Sordelli, Fernanda R Buzzola, Wondwossen A Gebreyes, Juliano L. Gonçalves, Marcos V. dos Santos, Zunita Zakaria, Vera L. M. Rall, Orla M. Keane, Dagmara A. NiedzielaGavin Paterson, Mark A. Holmes, Thomas C Freeman, Ross Fitzgerald*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host-adaptation, expansion and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around
the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 years ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialisation and industrialisation of dairy farming, and older lineages have become globally-distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pan-genome network
analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine associated genes, consistent with multiple trajectories to host-adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic and gene-level perspective of its remarkable success.
Original languageEnglish
Article numbere2211217119
Pages (from-to)1-11
Number of pages11
JournalProceedings of the National Academy of Sciences (PNAS)
Issue number50
Early online date5 Dec 2022
Publication statusE-pub ahead of print - 5 Dec 2022

Keywords / Materials (for Non-textual outputs)

  • Staphylococcus aureus
  • population genomics
  • phylodynamics
  • agriculture
  • host-adaptation


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