Initial safety evaluation of Enterococcus faecium LBB.E81

Due to their antimicrobial activity Enterococcus faecium strains have a growing record of use as beneficial adjunct cultures in animal nutrition or components of probiotic preparations for humans. However, safety concerns accompany the application of enterococci, as clinical strains associated with infection have been isolated, especially antibiotic resistant cultures. With the increasing availability of whole genome sequencing (WGS), valuable safety data can be extracted in the early phase of development of the probiotic dossier of an E. faecium strain. Here we report the results of initial safety assessment of E. faecium LBB.E81 by selecting accessible commercial antibiotic susceptibility test and WGS. Testing against a panel of antibiotic substances showed that E. faecium LBB.E81 was susceptible to all antimicrobials with the exception of its intrinsic, non-transferable resistance to nitrofurantoin. The identified antibiotic resistance genes of E. faecium LBB.E81 aac(6')-Ii, msrC and efmA belonged to a group of intrinsic non-transferable factors contributing to the lower susceptibility of the E. faecium species to aminoglycoside and macrolide antibiotics but with minimal inhibitory concentrations for E. faecium LBB.E81 below the threshold values determined for resistant strains. The only potential virulence factor genes found in the genome of E. faecium LBB.E81 were a defective acm (collagen-binding adhesin) and efaA (fm) (antigen A - like protein) without any evidence for its involvement in pathogenicity. Other hospital associated virulence factor genes of E. faecium such as IS16, hyl, asa-type genes, cyl; gelE and fsr, sprE and esp(fm) were found to be absent in E. faecium LBB.E81.

Automated summary

Enterococcus faecium strains are being increasingly used as beneficial cultures in animal nutrition and probiotic preparations for humans due to their antimicrobial activity. However, concerns about safety and antibiotic resistance have been raised. Through commercial antibiotic susceptibility tests and whole genome sequencing, valuable safety data can be extracted to assess the safety and potential resistance of E. faecium strains.