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Engineered viruses could fight drug resistance

Engineered viruses could fight drug resistance

In the battle against antibiotic resistance, many scientists have been trying to deploy naturally occurring viruses called bacteriophages that can infect and kill bacteria.

Bacteriophages kill bacteria through different mechanisms than antibiotics, and they can target specific strains, making them an appealing option for potentially overcoming multidrug resistance. However, quickly finding and optimizing well-defined bacteriophages to use against a bacterial target is challenging.

In a new study, MIT biological engineers showed that they could rapidly program bacteriophages to kill different strains of E. coli by making mutations in a viral protein that binds to host cells. These engineered bacteriophages are also less likely to provoke resistance in bacteria, the researchers found.

“As we’re seeing in the news more and more now, bacterial resistance is continuing to evolve and is increasingly problematic for public health,” says Timothy Lu, an MIT associate professor of electrical engineering and computer science and of biological engineering. “Phages represent a very different way of killing bacteria than antibiotics, which is complementary to antibiotics, rather than trying to replace them.”

The researchers created several engineered phages that could kill E. coli grown in the lab. One of the newly created phages was also able to eliminate two E. coli strains that are resistant to naturally occurring phages from a skin infection in mice.

Lu is the senior author of the study, which appears in the Oct. 3 issue of Cell. MIT postdoc Kevin Yehl and former postdoc Sebastien Lemire are the lead authors of the paper.

Engineered viruses

The Food and Drug Administration has approved a handful of bacteriophages for killing harmful bacteria in food, but they have not been widely used to treat infections because finding naturally occurring phages that target the right kind of bacteria can be a difficult and time-consuming process.

To make such treatments easier to develop, Lu’s lab has been working on engineered viral “scaffolds” that can be easily repurposed to target different bacterial strains or different resistance mechanisms.

“We think phages are a good toolkit for killing and knocking down bacteria levels inside a complex ecosystem, but in a targeted way,” Lu says.

In 2015, the researchers used a phage from the T7 family, which naturally kills E.coli, and showed that they could program it to target other bacteria by swapping in different genes that code for tail fibers, the protein that bacteriophages use to latch onto receptors on the surfaces of host cells.

While that approach did work, the researchers wanted to find a way to speed up the process of tailoring phages to a particular type of bacteria. In their new study, they came up with a strategy that allows them to rapidly create and test a much greater number of tail fiber variants.

From previous studies of tail fiber structure, the researchers knew that the protein consists of segments called beta sheets that are connected by loops. They decided to try systematically mutating only the amino acids that form the loops, while preserving the beta sheet structure.

“We identified regions that we thought would have minimal effect on the protein structure, but would be able to change its binding interaction with the bacteria,” Yehl says.

They created phages with about 10,000,000 different tail fibers and tested them against several strains of E. coli that had evolved to be resistant to the nonengineered bacteriophage. One way that E. coli can become resistant to bacteriophages is by mutating “LPS” receptors so that they are shortened or missing, but the MIT team found that some of their engineered phages could kill even strains of E. coli with mutated or missing LPS receptors.

This helps to overcome one of the limiting factors in using phages as antimicrobials, which is that bacteria can generate resistance by mutating receptors that the phages use to enter bacteria, says Rotem Sorek, a professor of molecular genetics at the Weizmann Institute of Science.

“Through deep understanding of the biology entailing the phage-bacteria recognition, together with smart bioengineering approaches, Lu and his team managed to design a large library of phage variants, each of which has the potential to recognize a slightly different receptor. They show that treating bacteria with this library rather than with a single phage limits the emergence of resistance,” says Sorek, who was not involved in the study.

Other targets

Lu and Yehl now plan to apply this approach to targeting other resistance mechanisms used by E. coli, and they also hope to develop phages that can kill other types of harmful bacteria. “This is just the beginning, as there are many other viral scaffolds and bacteria to target,” Yehl says. The researchers are also interested in using bacteriophages as a tool to target specific strains of bacteria that live in the human gut and cause health problems.

“Being able to selectively hit those nonbeneficial strains could give us a lot of benefits in terms of human clinical outcomes,” Lu says.

The research was funded by the Defense Threat Reduction Agency, the National Institutes of Health, the U.S. Army Research Laboratory/Army Research Office through the MIT Institute for Soldier Nanotechnologies, and the Koch Institute Support (core) Grant from the National Cancer Institute.

Materials provided by Massachusetts Institute of Technology

Urine cultured on Oxoid Brilliance UTI Agar plate

Harnessing Zinc would help to cure UTI without antibiotics

UTIs are one of the prominent bacterial infections across the globe, with about 150 million cases each year, and can lead to serious health problems like chronic kidney infection (pyelonephritis) and sepsis.

Recently in a study, it was found that zinc can play a vital role in the development of new non-antibiotic treatment strategies for UTIs using our immune system.

The study was done by the researchers, including members of the IMB (Institute for Molecular Bioscience) – Professor Matt Sweet, Dr. Ronan Kapetanovic and Claudia Stocks, and members of UQ’s School of Chemistry and Molecular Biosciences  – including Professor Mark Schembri and Dr. Minh-Duy Phan, examined how our immune system uses zinc to fight against bacterial infections.

“We confirmed by direct visualization that cells in our immune system known as macrophages deploy zinc to clear bacterial infections,” said Dr. Minh Duy from UQ’s School of Chemistry and Molecular Biosciences.

“We found that, compared to non-pathogenic bacteria, UPEC can evade the zinc toxicity response of macrophages, but these bacteria also show enhanced resistance to the toxic effects of the zinc.
These findings give us clues to how our immune system battles infections, and also potential avenues to develop treatments, such as blocking UPEC’s escape from zinc to make it more sensitive to this metal.”

The team developed new systems to track and analyze the insertion of zinc in macrophages, with this work just published in Proceedings of the National Academy of Sciences USA (PNAS USA).

They found that, compared to non-pathogenic E. coli, UPEC has a two-pronged strategy to survive the body’s immune response. It can prevent the delivery of zinc by hiding within the macrophage itself.

E Coli Bacteria

Colorized scanning electron micrograph of Escherichia coli, grown in culture and adhered to a cover slip. Source: https://www.flickr.com/photos/niaid/16578744517/

“We knew that UPEC can escape from the normal digestion pathway of the macrophage.
Our latest results show that UPEC can also avoid the delivery of zinc by hiding in different niches in these cells,” Dr. Kapetanovic said.
“It’s now clear that UPEC’s ability to occupy these specific compartments is an important factor in allowing it to spread through the body to cause severe disease.”

But evasion isn’t UPEC’s only trick. The team also found that UPEC has an enhanced ability to resist zinc toxicity.

“When we looked at UPEC, we found that they can also resist the toxic effects of zinc better than other bacteria,” Dr. Kapetanovic said.
“Taken together, these results may provide some potential avenues to develop treatments to combat UPEC and the diseases it causes, such as UTIs and sepsis. For example, blocking UPEC’s escape from zinc to make it more sensitive to this metal could help the body fight back.”

Professor Schembri and Dr. Phan used a technology called TraDIS to identify the full suite of UPEC genes involved in zinc resistance. Some of these genes had previously been explored, but a large number of others had not been explored for their involvement in protecting against zinc pressure.

Dr. Phan said, “The TraDIS analysis had given the researchers a map of which genes they could potentially target to make them more sensitive to zinc”. The team particularly focused on a type of cell called macrophage.

“Macrophages are key immune cells in the body. They digest and destroy a variety of different pathogens, have many strategies to do this, some of which are very well known and some that we’re really only discovering now.

One such recently discovered macrophage antimicrobial response uses zinc poisoning to kill bacteria, so we investigated how macrophages deploy zinc against UPEC.” said Miss Stocks.

“In creating this tool, we’ve not just found out more about E. coli, but have also created a model to study different types of bacteria, bringing us closer to not only understanding our immune system better but also to creating therapies for a range of infectious diseases.

Macrophages deploy zinc against persistent bacteria that aren’t necessarily being cleared by normal mechanisms, for example, Mycobacterium tuberculosis, Salmonella and Streptococcus; all bacteria that can cause chronic infections,” Miss Stocks said.

The new research doesn’t just have after effects for UPEC and  UTIs they cause. The team has also developed zinc sensors that could be used to study a variety of disease-causing bacteria.