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Resistance of hospital-associated bacterium traced back to mid-19th century

An international research team has discovered that Enterococcus faecalis, a bacterium largely responsible for infections acquired in hospitals, had adapted to hospital conditions long before the emergence of modern healthcare institutions.


In the last few decades, enterococci have become a major cause of hospital-acquired infection. Of these bacteria, E. faecalis bears a large share of the responsibility for human enterococcal infections in hospitals and is furthermore one of the most antibiotic-resistant types of bacteria. An international research team supported by the EU-funded SCARABEE and SCIENTIA-FELLOWS II projects has now identified the features of E. faecalis that have helped it to survive despite modern advances in antibiotic development and infection control in healthcare settings. The team’s findings were published in the journal ‘Nature Communications’. Typically found in the gut and bowel, E. faecalis can cause infection when it enters a wound, the blood or urine, with patients in hospitals more at risk of infection because of their weakened immune systems. The bacteria can contribute to infections such as blood poisoning, inflammation of the heart’s inner lining and enterococcal meningitis. The researchers studied E. faecalis samples taken from a wide variety of host species, including wild birds, mammals, healthy people and hospitalised patients, and ranging from the pre-antibiotic era in 1936 to 2018. Short- and long-read DNA sequencing techniques were used to sequence the bacterial genomes. “We had a rare opportunity to study clinical specimens from the time before the wide introduction of antibiotics,” explains co-author Prof. Jukka Corander in a press release posted on the University of Helsinki website. “The oldest sample we analysed was taken in a Dutch hospital in 1936. Determining the exact genome of these old bacteria gave us a chance to compare them with modern clinical specimens and trace the evolution of the bacterial population with unbelievable precision,” continues Prof. Corander, who is affiliated with the University of Oslo and the University of Helsinki.

The oldest hospital-associated E. faecalis lineages

The study reported multiple lineages of E. faecalis worldwide that are associated with hospitals. Their last common ancestors date back as far as the mid-19th century, which is long before the emergence of modern hospital environments. “There were no antibiotics or similar antibacterial solutions available in the 19th century as in modern hospitals. And yet, a selective pressure of some kind led to the birth of these bacterial strains. Thanks to the features added to their genome, the bacteria continue to survive and spread in hospitals to this day,” Prof. Corander reports. The team found genes in the old E. faecalis samples that made the bacteria resistant to arsenic and mercury, identifying these elements as likely external selective pressures. Of all the samples taken, the wild bird species specimens were particularly intriguing. “We found E. faecalis strains in the faeces of a number of wild birds, which were similar to the strains specialised to hospitals. Since most of the samples were taken from bird species that are not in close contact with human populations, we can conclude that the traits that make strains associated with hospitals successful provide them with the ability to live and spread also in bird populations.” The study highlights the importance of monitoring patients in hospitals to detect hospital-associated enterococcal strains as early as possible and prevent their transmission. SCARABEE (Scalable inference algorithms for Bayesian evolutionary epidemiology) and SCIENTIA-FELLOWS II (SCIENTIA-FELLOWS II: International Postdoctoral Fellowship Programme) are both coordinated by the University of Oslo. They end in 2022 and 2024, respectively. For more information, please see: SCARABEE project SCIENTIA-FELLOWS II project


SCARABEE, SCIENTIA-FELLOWS II, Enterococcus faecalis, E. faecalis, bacteria, hospital, infection

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22 August 2019