Having bacteria produce their own venom

It is a tour de force. Carbapenems are lethal to bacteria. Yet Delft researchers have succeeded in designing the bacterium E.coli to produce the chemical in quantities that are promising for large-scale production. They have engineered bacteria to produce a simple carbapenem called ‘Car’. Their work is published in the journal Nature Chemical Biology.

The researchers borrowed a few genes that are known to be responsible for the production of Car from another microorganism called P. carotovorum and introduced these genes into E. coli. Introducing the Car genes into E. coli did indeed result in the bacteria producing the antibiotic, but only in small amounts. The most significant bottleneck was an inefficient enzyme. The researchers introduced an additional gene into E. coli to produce a protein that helps this enzyme become more active.

The first author of the paper is Helena Shomar of the Bionanoscience department. “We noticed that because of the toxic effects of Car, our engineered bacteria were dying rapidly. Indeed, carbapenems disrupt the formation of the cell wall when bacteria multiply, ultimately causing the bacteria to explode,” she explains. “But if the bacteria do not reproduce, these antibiotics have a far less effect on them. So we have designed a genetic mechanism to stop our E. coli cells from multiplying. We simply inhibited one of the chemical pathways in the cell that produce components required to make the cell membrane. We use a sort of genetic switch to control when the cells multiply and when they stop multiplying and start producing the antibiotic.”

‘We hope to produce new carbapenems that do not yet exist in nature’

“Our engineered E. coli are a proof of concept,” Shomar says. “We were able to produce about 50 milligrams of Car per litre of bacterial suspension. It is promising. It is 10 times more than previous efforts to produce carbapenems with bacteria. Yet, for it to be commercially viable we need to increase production to at least one gram per litre. Our experiments were done in laboratory flasks and with a small amount of cells. We are confident that we can further increase production by scaling-up our process by using our bacteria in a bioreactor.”

Why would this be so much better compared to the current carbapenem production method based on chemical synthesis? “That technique is very expensive, elaborate and polluting. But so far it has been the only way the industry manages to produce these antibiotics at large-scale.”

What also makes the newly developed biological process interesting is the fact that, in theory, researchers could generate new kinds of Carbapenem antibiotics by introducing new enzymes in E. coli. “We hope that at some point this approach will be used to produce new carbapenems that do not yet exist in nature. This is largely unexplored territory.”