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Enterococci have emerged as important opportunistic pathogens in intensive care units (ICUs). In this study, enterococcal population size and  Enterococcus  isolates colonizing the intestinal tract of ICU patients receiving Selective Digestive Decontamination (SDD) were investigated. All nine patients included in the study showed substantial shifts in the enterococcal 16S rRNA gene copy number in the gut microbiota during the hospitalization period. Furthermore, 41  Enterococcus  spp. strains were isolated and characterized from these patients at different time points during and after ICU hospitalization, including  E. faecalis  ( n  = 13),  E. faecium  ( n  = 23), and five isolates that could not unequivocally assigned to a specific species ( E. sp. n  = 5) Multi locus sequence typing revealed a high prevalence of ST 6 in  E. faecalis  isolates (46%) and ST 117 in  E. faecium  (52%). Furthermore, antibiotic resistance phenotypes, including macrolide and vancomycin resistance, as well as virulence factor-encoding genes [ asa1, esp - fm, esp - fs, hyl , and  cyl  (B)] were investigated in all isolates. Resistance to ampicillin and tetracycline was observed in 25 (61%) and 19 (46%) isolates, respectively. Furthermore, 30 out of 41 isolates harbored the  erm  (B) gene, mainly present in  E. faecium  isolates (78%). The most prevalent virulence genes were  asa 1 in  E. faecalis  (54%) and  esp  ( esp-fm , 74%;  esp-fs , 39%). Six out of nine patients developed nosocomial enterococcal infections, however, corresponding clinical isolates were unfortunately not available for further analysis. Our results show that multiple  Enterococcus  species, carrying several antibiotic resistance and virulence genes, occurred simultaneously in patients receiving SDD therapy, with varying prevalence dynamics over time. Furthermore, simultaneous presence and/or replacement of  E. faecium  STs was observed-, reinforcing the importance of screening multiple isolates to comprehensively characterize enterococcal diversity in ICU patients.

frontiers in microbiology

Characterization of Enterococcus Isolates Colonizing the Intestinal Tract of Intensive Care Unit Patients Receiving Selective Digestive Decontamination