We report the occurrence and genomic features of multidrug-resistant vancomycin-resistant Enterococcus faecium vanA belonging to a novel sequence type (designated ST1336), carrying a Tn1546-like element, in marine brown mussels (Perna perna) from anthropogenically affected coastal waters of the Atlantic coast of Brazil, highlighting a potential source of dissemination for related ecosystems, with additional consequences for seafood safety and quality. •Occurrence of vancomycin-resistant Enterococcus faecium in wild mussels has been investigated.•Identification of VanA-type E. faecium (VREfm) ST1336 is highlighted.•Genomic analysis revealed a Tn1546-like element, previously reported in human and environmental strains.•Contamination of seafood by VREfm in an impacted ecosystem has been discussed.