Evolutionary Insights into CC17 Enterococcus faecium

Abstract

Enterococci are known to be intrinsically resistant to many antibiotics, but also acquire new resistance traits readily, rendering most clinical enterococci multi-resistant. Though initially considered as a relatively harmless commensal, the enterococci have attracted increased public and clinical interest since the first identification of vancomycin-resistant enterococci (VRE) in 1986. In the USA, VRE epidemiology was initially characterized by sporadic, but rapidly increasing monoclonal nosocomial outbreaks, eventually resulting in a polyclonal endemic situation in US hospitals and long-stay health care facilities. Currently, VRE are the third leading cause of bloodstream infections. Since the turn of the century, VRE prevalence has also been rising in European hospitals. In parallel with this increase in nosocomial VRE infections, the proportion of E. faecium infections has increased relative to those of Enterococcus faecalis. Epidemiology and initial molecular epidemiological studies suggested the presence of a genetic subset of VRE prevalent in hospitals worldwide. In the present thesis we describe, using different genetic typing methods, the presence of a worldwide subset of hospital adapted ampicillin resistant E. faecium, irrespective of vancomycin resistance. With multi-locus sequence typing, the gold standard for characterization of population structures, this subset was defined clonal complex 17. Mutations in the E. faecium quinolone resistance determining region, resulting in high-level ciprofloxacin resistance, were confined to CC17 strains. In addition to specific antibiotic resistance types, the E. faecium variant enterococcal surface protein, esp, was present in approximately 60% of CC17 strains, and proved to be part of a putative pathogenicity island. Comparative genomic hybridizations revealed more than 100 CC17-specific genes, most likely acquired through horizontal gene transfer. A majority of these genes clustered in two major genomic regions, nevertheless the other genes were located scattered over the bacterial genome. IS elements were highly prevalent among CC17 specific genes, possibly resulting in observed increased CC17 genome plasticity. Acquisition of these CC17 specific genes, most probably, has occurred multistep-wise and has been pivotal in the progression of E. faecium from an enteric commensal towards a hospital-adapted pathogen, thus enabling the acquisition of yet more adaptations. The population structure of the other major enterococcal nosocomial pathogen E. faecalis, shows presence of several clonal complexes enriched with clinical isolates. It was already known that these enterococcal species carry identical resistance cassettes; inaddition, E. faecium CC17 specific genes were identified among several invasive E. faecalis strains. A subset of these clustered together on E. faecalis mobile element, EfaB5, containing putative virulence genes. Sharing the same hospital niche, these two enterococcal species, therefore, might also exchange virulence genes. Identification of CC17 specific traits, could lead to development of specific laboratory tests and new CC17-selective drugs and vaccines, for rapid identification, eradication and treatment of infections caused by CC17 E. faecium.