Comparative genomics of Enterococcus cecorum UK isolates
Enterococcus cecorum has emerged as a significant poultry pathogen, causing musculoskeletal infections and increased mortality. Its epidemiology involves both vertical and horizontal transmission, influenced by management practices. Additionally, it harbours antimicrobial resistance (AMR) genes, raising concerns about multidrug resistance. Although genomic studies on E. cecorum have been conducted globally, no research has specifically examined isolates from the UK.This study analysed 123 UK E. cecorum isolates (2003–2022) alongside 102 non-UK isolates, assessing phylogeny, AMR, and virulence. Whole-genome sequencing and SNP analysis identified eight major UK lineages with limited intra-lineage variation, suggesting strain persistence. A 60-SNP threshold delineated 18 clusters, indicating recurrent transmission. UK isolates carried fewer AMR genes than non-UK ones, with erm(B), lnu(C), tet(M), and tet(L) most prevalent. Co-localization of tet(M) and tet(L) suggest horizontal gene transfer. Putative virulence determinants analysis linked specific genes to pathogenicity in 24 isolates. Multiple statistical approaches, including random forest models, highlighted key virulence-associated genes, aligning with prior studies. However, variability across methods suggests pathogenicity is influenced by multiple genetic factors rather than single genes. When putative virulence determinants analysis was applied to all UK isolates (clinical origin) in our panel, these 12 genes alone were not able to fully differentiate pathogenic from commensal strains. While this study provides valuable insights, further validation with a larger dataset, including commensals, would enhance the robustness and generalisability of the findings beyond the current sample size (n=24)..  This first genomic characterisation of UK E. cecorum highlights its phylogenetic diversity, AMR burden, and virulence potential, underscoring the need for enhanced biosecurity, targeted surveillance, and further functional validation.