Comparison of Enterococcus cecorum using genomic and mass spectra analyses

E. cecorum (EC) is a commensal but also a major pathogen for fast-growing broilers worldwide. Thus, differentiation between 'clinical' or 'non-clinical' strain status is of first interest. The aim of this study was to perform a molecular comparison of 'clinical' and 'non-clinical' strains collected within a restricted timeframe and geographical area. During 2023 and 2024, 54 strains were collected in Brittany. Protein fingerprints obtained by MALDI-TOF allowed the grouping of strains into subgroups based on their degree of similarity, from which six pairs of strains were selected. Whole-genome sequencing (WGS) was performed, and genome analysis was used to search for the presence of virulence factors (VF) and to perform a single nucleotide polymorphism (SNP) analysis. Despite a selection of specific EC biomarkers, MALDI-TOF analysis was unable to differentiate between 'clinical' and 'non-clinical' strains. SNP analysis revealed significant genetic diversity between strains belonging to different subgroups. Surprisingly, only minor differences were observed within each pair comprising one 'clinical' and one 'non-clinical' strain (58, 76, and 690 SNPs). No differences were observed in the VF profiles of the paired strains, unlike what was observed between the subgroups. High EC genomic diversity was observed. Genetic differences between the strains have resulted in a type of classification that does not align with clinical criteria. Therefore, molecular determinants of 'clinical' strains have not been confirmed. These results would suggest that EC is an opportunistic agent that can exhibit different pathogenic outcomes depending on external factors.