P09 Genomic characterization of nasal Enterococcus faecalis carrying linezolid resistance in healthy hosts identifies zoonotic transmission

TL;DR

This study finds linezolid-resistant Enterococcus faecalis in humans and animals, suggesting zoonotic transmission and the need for better surveillance.

Contribution

The study identifies genomic features and transmission patterns of linezolid-resistant E. faecalis in healthy hosts and animals.

Findings

Linezolid-resistant E. faecalis strains were found in pigs, pig farmers, and a dog.

SNP analysis showed close genetic relatedness between strains from animals and humans.

All strains carried multiple virulence genes and resistance genes on plasmids.

Abstract

Linezolid resistance in Enterococcus faecalis (a normal gut bacterium) is increasingly considered a critical public health concern, hence the need to understand their genomic contents and dissemination patterns.

Illumina-based sequencing was used to characterize seven linezolid-resistant (LZDR) E. faecalis strains obtained from the nares of healthy humans and animals in Spain. Also, the relatedness of the strains with publicly available genomes of E. faecalis with similar lineages and AMR determinants was accessed by core-genome SNP analysis.

E. faecalis was identified in 32.5% of 40 pigs, 30% of 10 pig farmers, 5.9% of 34 dogs and 4.9% of the 41 dog owners. Of the E. faecalis strains, only five, one and one strains from pigs, a pig farmer and a dog, respectively, were optrA-positive. All the optrA were chromosomally located and variants (types 5, 7 and 15) except one that was a WT strain (from a pig). All the strains carried between 16 and 35 virulence genes associated with ≥1 intact prophage. All the enterococci carried ≥1 plasmid replicon (1–5) carrying tetracycline and chloramphenicol resistance genes. SNP-based analyses identified closely related E. faecalis strains from a pig and pig farmer on the same farm (SNP=4). Moreover, E. faecalis ST32, ST59 and ST474 strains from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43–86).

These findings strongly suggest the zoonotic transmission of LZDRE. faecalis and potential international dissemination. These highlight the need to strengthen molecular surveillance of linezolid-resistant enterococci in all ecological niches and body parts to direct appropriate control strategies.