University of Exeter researchers exposed E.coli bacteria to eight rounds of antibiotic treatment over four days and found that they hads peedier and increased antibiotic resistance with each treatment.
This had been expected, but researchers were surprised to find mutated E.coli reproduced faster than before encountering the drugs and formed populations that were three times larger because of the mutations.
This was only seen in bacteria exposed to antibiotics – and when researchers took the drug away, the evolutionary changes were not undone and the new-found abilities remained.
“Our research suggests there could be added benefits for E.coli bacteria when they evolve resistance to clinical levels of antibiotics,” said lead author Professor Robert Beardmore, of the University of Exeter. “It’s often said that Darwinian evolution is slow, but nothing could be further from the truth, particularly when bacteria are exposed to antibiotics.
“Bacteria have a remarkable ability to rearrange their DNA and this can stop drugs working, sometimes in a matter of days.
“While rapid DNA change can be dangerous to a human cell, to a bacterium like E.coli it can have multiple benefits, provided they hit on the right changes.”
The researchers tested the effects of the antibiotic doxycycline on E.coli as part of a study of DNA changes brought about by antibiotics. The E.coli “uber-bug” that subsequently evolved was safely frozen at -80C and the scientists used genetic sequencing to find out which DNA changes were responsible for its unusual evolution.
Some changes are well known and have been seen in clinical patients, like E.coli producing more antibiotic pumps that bacteria exploit to push antibiotics out of the cell.
Another change saw the loss of DNA that is known to describe a dormant virus.
“Our best guess is that losing viral DNA stops the E.coli destroying itself, so we see more bacterial cells growing once the increase in pump DNA allows them to resist the antibiotic in the first place,” said Dr Carlos Reding, who was part of the study.
“This creates an evolutionary force for change on two regions of the E.coli genome.
“Normally, self-destruction can help bacteria colonise surfaces through the production of biofilms. You see biofilms in a dirty sink when you look down the plughole.
“But our study used liquid conditions, a bit like the bloodstream, so the E.coli could give up on its biofilm lifestyle in favour of increasing cell production.”
Dr Mark Hewlett, also of the University of Exeter, added: “It is said by some that drug resistance evolution doesn’t take place at high dosages but our paper shows that it can and that bacteria can change in ways that would not be beneficial for the treatment of certain types of infection.
“This shows it’s important to use the right antibiotic on patients as soon as possible so we don’t see adaptations like these in the clinic.”
Abstract
Evolutionary trajectories are constrained by trade-offs when mutations that benefit one life history trait incur fitness costs in other traits. As resistance to tetracycline antibiotics by increased efflux can be associated with an increase in length of the Escherichia coli chromosome of 10% or more, we sought costs of resistance associated with doxycycline. However, it was difficult to identify any because the growth rate (r), carrying capacity (K) and drug efflux rate of E. coli increased during evolutionary experiments where the species was exposed to doxycycline. Moreover, these improvements remained following drug withdrawal. We sought mechanisms for this seemingly unconstrained adaptation, particularly as these traits ought to trade-off according to rK selection theory. Using prokaryote and eukaryote microorganisms, including clinical pathogens, we show that r and K can trade-off, but need not, because of ‘rK trade-ups’. r and K trade-off only in sufficiently carbon-rich environments where growth is inefficient. We then used E. coli ribosomal RNA (rRNA) knockouts to determine specific mutations, namely changes in rRNA operon (rrn) copy number, than can simultaneously maximize r and K. The optimal genome has fewer operons, and therefore fewer functional ribosomes, than the ancestral strain. It is, therefore, unsurprising for r-adaptation in the presence of a ribosome-inhibiting antibiotic, doxycycline, to also increase population size. We found two costs for this improvement: an elongated lag phase and the loss of stress protection genes.
Authors
Carlos Reding-Roman, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, Robert Beardmore
[link url="http://www.exeter.ac.uk/news/research/title_566715_en.html"]University of Exeter material[/link]
[link url="http://www.nature.com/articles/s41559-016-0050"]Nature Ecology & Evolution abstract[/link]