Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era

The enterococci evolved over eons as highly adapted members of gastrointestinal consortia of a wide variety of hosts, but for reasons that are not entirely clear, emerged in the 1970s as leading causes of multidrug resistant hospital infection. Hospital-adapted pathogenic isolates are characterized by the presence of multiple mobile elements conferring antibiotic resistance, as well as pathogenicity islands, capsule loci and other variable traits. Enterococci may have been primed to emerge among the vanguard of antibiotic resistant strains because of their occurrence in the GI tracts of insects and simple organisms living and feeding on organic matter that is colonized by antibiotic resistant, antibiotic producing micro-organisms. In response to the opportunity to inhabit a new niche — the antibiotic treated hospital patient — the enterococcal genome is evolving in a pattern characteristic of other bacteria that have emerged as pathogens because of opportunities stemming from anthropogenic change. ⺠Enterococci are ancient commensals in the GI tracts of hosts ranging from insects to man. ⺠Enterococci are now leading causes of multidrug resistant infection and are spreading resistances. ⺠Genomes of hospital adapted strains of enterococci consist of over 25% mobile elements. ⺠Loss of CRISPR protection of the genome correlates with the accumulation of resistance and virulence traits. ⺠Pathogens evolve from generalists by adapting to new ecologies created by anthropogenic change.