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MADISON, WI, United States

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 282.62K | Year: 2013

DESCRIPTION (provided by applicant): This application aims to test a new Scarab E. coli strain, MDS42pdu, for commercial fermentation to produce biopharmaceuticals, amino acids and biofuels. It is designed for a very low rate of point mutations and Insertion Sequence transposition, especially in the stress conditions of recombinant protein production. We propose here to study the impact on a fundamental problem of large scale fermentation: Darwinian evolution of bacteria in the fermenter toward loss of productivity. Random mutations occurring in culture can produce cells freed from the burden of product formation and these have a selective advantage. Soon these overtake the culture and reduce or eliminate productivity. In short, cultures deteriorate. Selection of mutations can also undermine product purity. We would like to slow or eliminate this degradation of performance to improve stability, quality and efficiency of current fed batch methods and possibly, to support a more continuous fermentation protocolin the future. The proposed studies use periodic total genomic sequencing of extended cultures to compare ordinary production strains with the new low mutation strain to see if the period of culture productivity before degradation is extended, and whetherwe can identify the types of mutations involved in performance degradation. The two aims propose periodic whole genome sequencing of serially transferred cultures in shake flasks to quantify inexpensively the performance of the low mutation strain in a wide variety of cases, to be followed by more detailed study using continuous flow fermentation. We anticipate that control cultures using ordinary E. coli strains will become non productive considerably more quickly than MDS42pdu. If this anticipated resultis found, we will determine the maximum number of generations before problems emerge in the new production sytem. If a greatly extended productive lifetime is achieved we will consider it a major milestone toward commercialization of our product for fed batch fermentation. Sequencing will also help determine whether additional mutational mechanisms may be active that could be beneficially inactivated in future work. An extremely long productive culture life will indicate the feasibility of a continuous fermentation process usig this strain. PUBLIC HEALTH RELEVANCE PUBLIC HEALTH RELEVANCE: This proposal further develops Scarab Genomics' Clean Genome(R) E. coli to engineer a genetically stable strain for use in fermentation processes for biomanufacturing. Improved stability will provide higher quality bio- products and extended culturing will lead to higher yields from more efficient and cheaper production.

Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 1.55M | Year: 2016

DESCRIPTION provided by applicant Scarab Genomics was founded to improve E coli as an industrial organism by genome engineering These strains have stable genomes since all prophages transposable and IS elements and the error prone repair systems were removed A recA version has always been provided as an option The goal of the Phase I project was to ascertain whether the changes already introduced are sufficient to realize extended or continuous fermentation Data gathered in Phase I show that we have indeed supported that hypothesis Data obtained using serial transfer with shake flasks met our criterion for production stability of days but only when the cultures were not induced This suggested the use of a two tank system with seed and production tanks To confirm this we performed actual fermentations using Scarab funds The results show that stable production of a test protein CRM can be extended at least days with no loss of productivity This is more than enough to justify a fold lowering of the cost of production with continuous flow rather than fed batch procedures that have been used in for manufacturing in E coli Continuous cultures were also analyzed by DNA sequencing and this was able to detect contamination as well as mutations and rearrangements This analysis also revealed that the Scarab strain competed well against contaminants in contrast to standard strains BL We are therefore proposing to take this system to the next level by developing a complete platform for continuous fermentation called C Flow The FDA has recently encouraged adoption of continuous manufacturing in the pharmaceutical industry and several large companies have recently signaled readiness to implement the change Our aim is to attack the bottom line of E coli fermentation by offering a simpler and cheaper process that will produce consistently higher quality bioproducts than fed batch fermentation Our proposal is to fully characterize the C flow system and work towards commercializing it by developing a prototype that fits in a standard ft hood One particularly useful feature will support optimization of fermentation parameters without the need to restart fermentation so the best possible performance can be quickly and inexpensively achieved by a user Other products such as pDNA will be tested in the C Flow system PUBLIC HEALTH RELEVANCE Continuous fermentation will bring great benefits of improved drug manufacturing efficiency as well as high and consistent drug product quality The FDA is encouraging efforts to implement this technology in the pharmaceutical industry Patients will have access to a wider range of quality medicines that are made more economically current technology permits

Scarab Genomics, Llc | Date: 2012-10-19

Reduced genome bacteria with improved genetic stability are provided. Also provided are methods of producing polypeptides using the reduced genome bacteria with improved genetic stability.

Methods for prophylaxis or treatment of sepsis in a subject are provided comprising administering to the subject a therapeutically effective dose of multiple deletion strain bacteria.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 1.75M | Year: 2011

DESCRIPTION (provided by applicant): Complications arising from pathogen infection incur a tremendous societal cost both in morbidity and mortality (as high as 50-60%), as well as in care and treatment estimated in billions of dollars. In susceptible patients, infection induces mis-regulation of the innate immune system that can culminate in systemic inflammation, severe illness and death. The development of probiotics with the capacity to dampen or modulate this response would have enormous value and numerous medical applications. Scarab Genomics has developed Clean Genome(r) E. coli strains that are devoid of all deleterious gene sequences and are tolerated better than existing strains in mammalian systems. Such reduced E. coli strains can provide immediate protection against a lethal dose of infecting bacteria as well as toxins in mice, presumably by suppressing the extreme inflammatory response, or by raising the level of preparedness of the innate immune system, or both. This protective effect has greatpotential for use in clinical populations, both as an intervention for serious infections including sepsis and septic shock, and as a prophylactic to reduce the chance of infection in at-risk patients. Ideally the treatment would provide universal protection against any pathogenic challenge. In Phase I of the proposal, feasibility parameters including dosing regimen, route of delivery and the ability of non-viable preparations to protect against sepsis will be examined. In Phase 2, Clean Genome(r) strains that contain alterations in membrane lipopolysaccharide (the bacterial component strongly associated with innate immune activation) will be evaluated for protection against sepsis. Further, we will determine whether protection by reduced genome strains extends to other Gram-negative bacterial strains. To establish clinical relevance, a mouse model will be used to demonstrate protection by Clean Genome(r) strains of lethal doses of pathogenic E. coli strains including O157:H7, a colonizing, Shiga toxin-producing strain. An additional protective strain that will be tested in this context is the E. coli strain Nissle 1917, which has been in use as a probiotic for many decades and which has the capacity of colonize the intestine. Nissle 1917 is currently undergoing genome- reducing deletions at Scarab that have been targeted to enhance its safety and stability. The development of Nissle 1917 as a probiotic against infection and sepsis will result in protective colonizing bacteria for oral delivery. Our core competence in the targeted reduction and modification of E. coli will enable us to develop probiotics for the treatment of infection and sepsis. PUBLIC HEALTH RELEVANCE: The impact of these Clean Genome(r) products on human health could be highly significant, reducing complications associated with surgery or antibiotic treatments. Protection is likely to extend to many other bacteria and viruses, providing innate protection against septic toxicity and/or ameliorating their pathology, resulting in substantialsavings in health care costs. Further, development costs would be much lower than for conventional drugs, and pharmaceutical production of clean bacteria would be economical and highly efficient.

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