Phenotypic and genomic analysis of the emerging poultry pathogen Enterococcus cecorum in UK isolates

The rate of Enterococcus cecorum infections within poultry (e.g. chickens, racing pigeons and Pekin ducks) has rapidly increased since they were initially reported in the UK and the Netherlands in 2002. E. cecorum can infect the free thoracic vertebra of chickens, often leading to carcass rejection at processing plants, incurring large economic costs to farmers. The environmental spread of this pathogen has been facilitated by high levels of antimicrobial resistance, as well as the emergence of divergent clonal lines with a higher pathogenic potential within poultry. Previous genomic studies have explored these characteristics within E. cecorum populations in both the USA and France. However, whether E. cecorum isolates in other countries show the same genomic traits remains unknown. In the present study, we investigate the properties of 190 E. cecorum isolates collected from UK broiler farms between 2021 and 2022. We report the MICs and epidemiological cutoff values for 32 antibiotics and analyse the genome sequence of 39 representative organisms from diseased or healthy broiler farms. We show that UK isolates present phenotypic signs of resistance for 26 antibiotics tested and show that clinical isolates are enriched in a single clade. These strains share properties with pathogenic strains from France and the USA, including conserved cell wall biosynthesis loci, as well as mobile genetic elements involved in the propagation of antibiotic resistance genes. Our results support the idea of a cross-continental spread of virulent E. cecorum.