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Enterococcus faecalis  and  faecium  with resistance to daptomycin and/or linezolid are emerging globally. We present the genomic characterization of daptomycin- and linezolid-resistant  E. faecalis  and  E. faecium  surveillance isolates from the United States, 2013–2016. Daptomycin resistance was low among  E. faecalis  (2/364, 0.5%) and  E. faecium  (17/344, 5%). The majority (71%, 12/17) of daptomycin-resistant  E. faecium  isolates belonged to the emerging ST736 clone and contained mutations in  liaFSR  and  cls  previously associated with resistance. However, 1/2  E. faecalis  and 3/17  E. faecium  did not contain these mutations previously associated with daptomycin resistance. Linezolid resistance was rare among  E. faecalis  (1/364, 0.3%) and  E. faecium  (2/344, 0.6%). These two  E. faecium  isolates, one of which was also resistant to daptomycin and vancomycin, contained the 23S rRNA nucleotide mutation (G2576T) associated with linezolid resistance. Long-read sequencing revealed the linezolid-resistant  E. faecalis  isolate contained chromosomal- and plasmid-encoded copies of  optrA . The chromosomal  optrA  was located on the recently described Tn 6674  multiresistance transposon. The second copy of  optrA  was encoded on an ∼65 kb mosaic plasmid, with component regions sharing high sequence identity to  optrA -encoding multiresistance plasmids of animal origin. The  optrA -encoding plasmid contained open reading frames predicted to encode proteins associated with a pheromone-responsive plasmid transfer system, and filter mating experiments confirmed the plasmid was conjugative. Continued surveillance of enterococci is necessary to assess the prevalence and trends of daptomycin and linezolid resistance in the United States, characterize resistance mechanisms and how they transfer, and monitor for emerging sequence types associated with resistance.

frontiers in microbiology

Sentinel Surveillance Reveals Emerging Daptomycin-Resistant ST736 Enterococcus faecium and Multiple Mechanisms of Linezolid Resistance in Enterococci in the United States