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Behind the doors of the bacterial factory

Published in Cosmos Magazine

By Ellen Phiddian

Excerpts copied below. Read the full article in Cosmos Magazine at the link at the bottom of the page.

BioCina’s pharmaceutical manufacturing plant, in Adelaide, is Australia’s only internationally certified microbial fermentation operation – and a lesson in keeping it clean. So how do they do it? Cosmos got an exclusive look inside the facility and a walk through the precise steps of using bacteria to make medicine.

First, of course, we have to wash our hands. Then we’re given washable fabric gowns, which cover every inch of skin between neck, wrists, and ankles. Next we don hair caps (and beard covers for those with beards). We exchange our shoes for specially cleaned facility shoes, with plastic covers, and add disposable gloves and goggles to our ensembles.

After that, we’re led to a room that only allows three people at a time, in order to keep the quality of the room environment highly controlled. A metal bench bisects the room. We take it in turns to sit and swivel over the bench, taking the shoe protectors off as we go – shoe covers are allowed exclusively on one side of the bench, and clean soles on the other. Out this door, and we’re able to collect the camera and microphone that we brought into the facility via a dedicated material and equipment entrance, both of which have been wiped down with alcohol. All other personal effects have been left behind in the locker room.

This is the level of precaution required to visit just the outer corridor of BioCina’s manufacturing wing.

Based in Thebarton, just outside Adelaide’s CBD, BioCina is currently the only place in Australia that has international certification to make commercial pharmaceuticals with microbes.

Putting bacteria to work

Microbial fermentation operates on a simple concept: genetically modify a bacterial strain, say E. coli, to make a molecule you want – often a protein, but it could be something else like plasmid DNA. Give the bacteria somewhere to multiply, and then – when you have enough – extract the molecule you’re after.

“We’re using bacterial cells as miniature factories to generate or produce pharmaceuticals,” summarises Anthony Morgan, Director of Operations at BioCina, as we survey a fermenter through a window doing just that.

It’s a simple theory, but in practice (as with anything that makes medicines), it requires a very, very high standard of scientific and manufacturing know how and capability to manufacture products that are effective and safe for use.

While it spent much of the last decade taking a back seat to mammalian cell culture, microbial fermentation was on its way back into the zeitgeist before 2020.

The COVID pandemic has hastened its return to prominence, for one simple reason: it’s how you make mRNA. Or rather, it’s the best way to make plasmid DNA and the enzymes that can turn that plasmid DNA into RNA.

BioCina isn’t making mRNA yet – it currently lacks the downstream resources to turn that mRNA into vaccines. The company put in a bid to the federal government’s approach to market last year, but lost out to Moderna’s proposed facility in Melbourne. At the moment, BioCina is continuing to make proteins, and they can make plasmid DNA for interested customers.

“We don’t own any IP,” says Ian Wisenberg, CEO of BioCina.

Instead, the facility operates on contracts. “We work with multiple customers on different programs, from vaccines to therapeutics, to nanobody programs,” says Wisenberg.

Some of this work can stay entirely in BioCina’s research and development section. But any potential product that gets into the manufacturing wing must also go through extensive safety testing, purity testing, and scaling up in R&D.

Everything else the bacteria and the product interacts with in the facility – sugars, salts, solutes and more – also has to meet a standard that’s considered safe to go in human bodies. Even if it doesn’t end up in the final product.

At BioCina, smaller amounts of these ingredients are stored in a just-in-time “big pantry” within the manufacturing wing, and turned into solutions that are used to manufacture the desired pharmaceutical product. This way, they’re ready to use when required during manufacture.

The making business

The manufacturing process itself is separated into three main parts: upstream fermentation, midstream processing, and downstream purification.

Fermentation is the first step. A vial of bacteria (usually E. coli, but other microbes could be used) is brought out from storage in a freezer (which keeps everything at a chilly -80°C). The vial is added to a larger flask and placed in an incubator, so it can multiply. BioCina’s skilled manufacturing team monitor this process closely until it’s ready to be added to the fermenter..

Once incubated, the flask is transferred through a port to a fermenter – anywhere in size between 20 to 500 litres, depending on how well the bacteria express the target molecule. The 500-litre stainless steel fermenter is two or three times the height of a person, and looks a little like a beer fermenter – with many, many more instruments, tubes and pipes coming out of it.

“We now want to make the cells extremely happy in this environment by providing optimal growth conditions,” says Morgan. This includes tweaking the nutrient supply, pH, temperature, and oxygen concentration, so that the microbes make as much of the target substance as possible.

When the bacteria have made plenty of the desired product, the liquid is transferred into midstream processing, and held in a 550-litre or 900-litre tank.

The microbes have done their job: the next step is to get rid of them. This is done first with a homogenizer: a “big blender” that destroys the bacterial cell walls. Then, a centrifuge is used to separate the mixture into its components, and harvest the target substance.

This whole process – fermentation and midstream processing – usually takes between three and five days, although timing can vary depending on the products and the manufacturing process requirements. Downstream purification takes another five to 10 days.

Downstream purification starts with fixing the protein’s shape – if it is a protein being made.

“Before we enter the downstream purification process, [we want to] return the target protein to its native conformational structure,” says Morgan.

In a 2,900-litre refolding tank, the protein is added to a solution where it can regain its original shape.

Now the game is to purify the substance further. This is done first with the tried-and-true scientific method of chromatography. The solution is pumped through a “column” of a solid resin, which has been chosen because it will stick to the target molecule. The column is then washed, and then the target molecule is forced off with another solution. Additional chromatography steps further improve the purity of the product.

This solution passes through a couple of filtration steps: ultrafiltration, to concentrate the solution down to a few litres, and diafiltration, which changes the solution holding the product into something that will store easily for a longer time.

The product is taken out of the manufacturing wing in big, single-use plastic bags. It is transferred and filtered into the “final ” containers – whichever container suits the products’ purpose – in a highly controlled filling suite and frozen. From here, it can be sent to a fill/finish facility (which bottles the product appropriately for distribution) anywhere in the world.

So very, very clean

On top of the strict requirements for personal wear, the facility has a range of other controls to keep clean. “From an operations perspective, a significant amount of time is invested in general facility cleaning, sanitising equipment and preparing equipment for processing,” says Morgan.

“That’s a big part of what we do. All of these walls, floors, ceilings, surfaces are regularly cleaned and maintained.”

The air temperature, pressure, and humidity has to stay stable and mostly free of particulates. The environment is monitored regularly for contamination, and all equipment entering the facility has to be sterilised in a person-sized autoclave.

It’s these regulations that give the TGA (and the US FDA, which many other countries use as a proxy) the confidence that this facility is making material that’s safe to go in human bodies.

Over the next decade, BioCina is unlikely to stay the only facility in Australia that can make commercial pharmaceuticals with microbes. The potential of mRNA alone is enticing enough, let alone other types of microbial manufacture.

“I know at least of more than 150 companies around the world that are working on an mRNA solution, whether it be a vaccine or therapeutic,” says Wisenberg.

But maintaining a plant like this demands decades of experience from highly skilled staff. Getting the approvals is a long and arduous process.

Doffing and disposing of my PPE after the walk through the facility, the thought that keeps running through my head is: there’s a huge difference between making something and making it cleanly.