August 1, 2016 (Vol. 36, No. 14)

Speculation That Microbial Fermentation May Overcome Mammalian Processing Is Premature

Benefits of microbial fermentation have stirred debate about it potentially overtaking mammalian processing. But the debate is more froth than substance. Microbial platforms won’t displace mammalian platforms anytime soon.

Microbial manufacturing is a critical part of the protein-expression industry mix, and it will remain so, particularly since the microbial side is growing. In fact, the microbial side is projected to grow even faster than the mammalian side in the coming years, although it should be pointed out that the microbial side is starting from a lower base.

Microbial manufacturing is growing because it presents certain advantages over mammalian processing. The main advantage is that microbial manufacturing is generally considered to be cheaper and quicker.

Besides this primary driver, microbial manufacturing can provide much higher upstream productivity. (This advantage, however, is partly negated by an associated disadvantage: lower purification yields.) Also, microbial manufacturing is expanding with the development of more advanced microbial expression systems and the emergence of products that are more conducive to microbial expression, such as antibody fragments.

Availability of Expertise

Most biopharmaceuticals are manufactured using mammalian systems, which are needed for the manufacture of most glycosylated proteins. Mammalian-expressed biopharmaceuticals include monoclonal antibodies, which have come to dominate both innovative and biosimilar products. The domimant position is being maintained by both pipeline and marketed products.

Nonetheless, microbial-expressed products are popular. In fact, they account for about 30% of the market for recombinant proteins. Supporting the microbial segment are at least 75 Escherichia coli-expressed products and around 25 yeast-expressed products.

Although microbial manufacturing is generally considered to be cheaper and simpler, it is not poised for dramatic growth. Microbial manufacturing remains inhibited by several factors. One problem is that many bioprocessing professionals, particularly in the United States, are now most knowledgeable about mammalian rather than microbial cell culture. Even in Europe, where most microbial expertise resides, mammalian systems are most familiar.

Trends in Capacity

Another factor tending to inhibit growth in microbial usage, at least in the United States, is the concentration of microbial capacity in Europe. For example, most large-scale GMP-capable contract manufacturing organizations (CMOs) reside in Europe. Meanwhile, GMP-capable CMOs in the United States lack sufficient microbial manufacturing capacity at over 100 L scales. Also, only recently have single-use microbial bioreactors started to enter the market.

Worldwide, there appears to be no shortage of microbial manufacturing capacity, and more capacity is being installed. According to a global survey conducted this year by BioPlan Associates, the biopharmaceutical industry maintains about 1,800 good-sized microbial bioreactors (≥100 L), including nearly 500 bioreactors near the higher-end (≥2,000 L).

These numbers come from BioPlan Associates’ 13th Annual Report and Survey of Biopharmaceutical Manufacturing Capacity and Production, the most recent study of biotherapeutic developers and contract manufacturing organizations’ current and projected future capacity and production. This report, which summarizes information from 222 bioprocessing professionals, indicates that overall microbial bioreactor capacity utilization (in terms of the percentage of operating capacity used) is 50.0%. In comparison, mammalian capacity utilization is higher, at 74.7%.

There appears to be no near-term microbial “capacity crunch.” Further, only 45.2% of respondents perform all their microbial production in-house, with most doing some outsourcing to CMOs.

Additional insights come from a quick powers-of-ten review of the survey’s numbers for production capacity. Of the survey’s respondents, 17.1% indicate that they maintain capacity below 100 L; 20%, from 100 to 999 L, 40%, from 1,000 to 9,999 L; and 22.9%, equal to and above 10,000 L. When the last three ranges are combined, it becomes apparent that 82.9% of respondents have capacity ≥100 L, sufficient for manufacture of most preclinical and early trial supplies. Also, it is notable that the largest portion of respondents, 40%, reported capacities in the 1,000 to 9,999 L range.

A closer look (Figure 1) reveals that 34.2% of respondents reported capacities of less than 500 L, a significant increase from 13.1% last year. The data suggest facilities have been adding bioreactors in the ≤500 L range. West European manufacturers continued to report significantly higher utilization rates for their microbial bioreactors (67%), compared to only 43.3% in the United States.

Figure 1. Percentage of respondents indicating pro-duction capacity ranges for microbial fermentation. This graphic provides the relative percentages of capacity, rather than total industry capacity. It provides insight into the relative scale of production capacities of individual firms in the industry.

Emergence of New Technology

Among the various microbial platforms, E. coli remains dominant. And E. coli protein expression in inclusion bodies (IBs) continues to dominate manufacturing, with about 85–90% capacity. More microbial users are seeking to avoid the refolding problems and lower purification yields associated with IBs, and are adopting newer E. coli soluble expression systems. Currently, soluble E. coli expression systems involve protein excretion into the cell cytoplasm. Likely, 10 years out, the vast majority of E. coli new processes will be secretory.

Commercially viable systems offering extracellular soluble protein expression, which promise to make downstream processing simpler and cheaper, are expected eventually. Other E. coli advances have yet to have major commercial impact, such as the fully single-use, plumbing-free MPTxpress system from MicroProtein Technologies. This system uses agar-gelled plates each producing ≥1 gram of protein paste overnight.

There will also be increased adoption of diverse non-E. coli platforms such as the Corynex platform, a Corynebacterium-based expression system from Ajinomoto Althea. These platforms offer downstream advantages. There are also platforms based on Pichia, Saccharomyces, and other yeasts, many of which are coming off-patent and are capable of incorporating glycosylation capabilities. Advances in expanded bed adsorption and other clarification and purification technologies will increase microbial yields, which remain much lower than with mammalian products.

These new microbial technologies will be part of the ecosystem that is pushing the growth in microbially produced biologics. But don’t expect the dominance of mammalian systems to be challenged anytime soon

Eric S. Langer ([email protected]) is president and managing partner
at BioPlan Associates.

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