Deciphering the Resistome and Mobiolme of an Avian-Associated <i>Enterococus faecalis</i> ST249 Clone that Acquired Vancomycin Resistance Isolated from Neutropenic Patient in Tunisia

This study aimed to characterize the first vancomycin-resistant <i>Enterococcus faecalis</i> (VREfs) isolate from patient with neutropenic in Tunisia by whole-genome sequencing (WGS). This strain was detected from routine rectal swab from an 8-year-old child with bone marrow aplasia, residing in a rural area, on September 20, 2021. The strain was isolated after 12 days of hospitalization at the National Bone Marrow Transplant Center. Minimum Inhibitory Concentrations of vancomycin and teicoplanin were >256 and 16 mg/L, respectively. WGS revealed that the strain belonged to the ST249 clone, exclusively reported in avian (poultry and ducks) vancomycin-susceptible <i>E. faecalis</i> isolates in six studies from four countries, primarily Denmark. The <i>vanA</i> gene was carried by the Tn<i>1546</i> transposon mobilized by a pTW9-like plasmid. The <i>ardA</i> gene, a CRISPR-Cas system neutralization factor, was detected in this strain. In summary, this is the first report of avian-associated <i>E. faecalis</i> ST249 in clinical samples. Initially vancomycin susceptible, the strain acquired a pTW9-like plasmid carrying the classical <i>vanA</i>-Tn<i>1546</i> transposon. This acquisition was facilitated by the sex pheromone-response mechanisms and the <i>ard</i>A gene and CRISPR-Cas system neutralization.