Mobile Menu

The genetic timeline of hospital superbug

Researchers at the Sanger Institute and their collaborators have explored, for the first time, the full evolutionary journey of hospital superbug – Enterococcus faecalis.


Generalist organisms can exploit multiple host taxa and habitat types. Whereas, specialist organisms are limited to only one or a few. Although generalist organisms can utilise different habitats, the ability to maintain homeostasis across diverse environments increases costs. The level of plasticity in particular traits will determine whether they can persist in different habitats. The study of bacterial pathogens and the molecular drivers of traits that associate with lifestyle, or jump between habitats or host types, has attracted a lot of interest.

Enterococcus faecalis is a commensal and nosocomial pathogen, found in the intestinal tract. It is ubiquitous in animals and insects, representing a classical generalist microorganism. Previous studies have shown a notable expansion of genome size by phages, mobile genetic elements and pathogenicity island to be associated with multi-drug resistant and hospital-adapted phenotypes in both E. faecium and E. faecalis. Nonetheless, these studies have been limited in their temporal span and coverage of different host species.

In this study, published in Nature Communications, researchers used a collection of 2,027 whole-genome sequences from E. faecalis isolates. The team wanted to obtain a picture of the gains and losses of plasmids in the population and the genome changes that allow this species to adapt to different ecologies. These isolates ranged from the pre-antibiotic era in 1936 up to 2018, from a large set of host species, including wild birds, mammals, healthy humans and hospitalised patients.

Timeline of hospital superbug

The team found that this bacterium has the ability to adapt very quickly to selection pressures. For example, the use of chemicals in farming and the development of new medications. These pressures have caused different strains of the same bacterium to be discovered in many places worldwide. Furthermore, as it is widespread, the researchers emphasised the importance of screening people in hospitals for this type of bacteria. This approach is already undertaken for other superbugs to help reduce the possibility of developing and spreading infection.

They found that antibiotic resistant strains of the bacterium developed earlier than previously thought, before the widespread use of antibiotics. Therefore, this indicates that it is not antibiotic use alone that caused these strains to emerge. Moreover, strains similar to the antibiotic resistant variants we find in hospitals now, were also found in wild birds. This highlights how adaptable and flexible this species of bacterium is at evolving into new strains.

Dr Anna Pöntinen, co-lead author and post-doctoral fellow at University of Oslo, expressed:

“Currently, when patients are admitted to hospital, they are swabbed for some antibiotic resistant bacteria and fungi and are isolated to ensure that infection rates are kept as low as possible. Thanks to this study, it is possible to scrutinise the diversity of E. faecalis and identify those that are more prone to spread within hospitals and thus could cause harm in immunocompromised people. We believe that it could be beneficial to also screen for E. faecalis on admission to hospitals.”

Image credit: By Science Photo Library –

More on these topics

Microbiology / Pathology / Superbug