fThe diversity of enterococcal populations from fecal samples from hospitalized (n ؍ 133) and nonhospitalized individuals (n ؍ 173) of different age groups (group I, ages 0 to 19 years; group II, ages 20 to 59 years; group III, ages >60 years) was analyzed. Enterococci were recovered at similar rates from hospitalized and nonhospitalized persons (77.44% to 79.77%) of all age groups (75.0% to 82.61%). Enterococcus faecalis and Enterococcus faecium were predominant, although seven other Enterococcus species were identified. E. faecalis and E. faecium (including ampicillin-resistant E. faecium) colonization rates in nonhospitalized persons were age independent. For inpatients, E. faecalis colonization rates were age independent, but E. faecium colonization rates (particularly the rates of ampicillin-resistant E. faecium colonization) significantly increased with age. The population structure of E. faecium and E. faecalis was determined by superimposing goeBURST and Bayesian analysis of the population structure (BAPS). Most E. faecium sequence types (STs; 150 isolates belonging to 75 STs) were linked to BAPS groups 1 (22.0%), 2 (31.3%), and 3 (36.7%). A positive association between hospital isolates and BAPS subgroups 2.1a and 3.3a (which included major ampicillin-resistant E. faecium human lineages) and between community-based ampicillin-resistant E. faecium isolates and BAPS subgroups 1.2 and 3.3b was found. Most E. faecalis isolates (130 isolates belonging to 58 STs) were grouped into 3 BAPS groups, BAPS groups 1 (36.9%), 2 (40.0%), and 3 (23.1%), with each one comprising widespread lineages. No positive associations with age or hospitalization were established. The diversity and dynamics of enterococcal populations in the fecal microbiota of healthy humans are largely unexplored, with the available knowledge being fragmented and contradictory. The study offers a novel and comprehensive analysis of enterococcal population landscapes and suggests that E. faecium populations from hospitalized patients and from community-based individuals differ, with a predominance of certain clonal lineages, often in association with elderly individuals, occurring in the hospital setting.
Enterococci are relatively minor constituents of the human gastrointestinal microbiota (less than 1%) but are able to cause a wide diversity of infections, mostly in patients with underlying diseases (1, 2). High-density colonization by antibiotic-resistant enterococci increases the risk of bacteremia and transmission; however, the population structure and ecological and evolutionary forces influencing the population dynamics of gut colonizers largely remain unknown (3-5). Next-generation sequencing has provided a wealth of data about the influence of characteristics of the host (age, diet, health status, and antibiotic treatment) on the diversity and population frequency of different bacterial groups, including enterococci (6-10). However, the information provided by current metagenomic analysis, based on 16S rRNA (11, 12), or by the traditi...