Charles River Laboratories [NYSE: CRL]

Jessica Wilson Rayse

Sterility Assurance Authority

Pharmaceutical and consumer care companies share the ultimate goal of producing a product safe for consumption, free of harmful microorganisms that cause disease or negatively impact the product. Contaminated products can result in patient illness, product recalls, drug shortages, damage to brand reputation, financial losses, and even criminal proceedings.

Given the negative consequences of contamination and product recalls, manufacturers should develop and be committed to a contamination control strategy. This consists of utilizing all the knowledge and experience of science and manufacturing to design and implement controls to prevent contamination. This strategy should be considered for all equipment, personnel, materials, procedures, processes, and facilities. As such, the contamination control strategy should be developed by a cross-functional group of people. Central to the contamination control strategy is knowledge of microbiology.

By understanding what organisms are present and at what level they are located in the manufacturing environment, controls can be put in place to protect the product from contamination. The most effective way to do this is to track and trend bioburden counts and microbial identifications. This acts as an early warning surveillance system by allowing you to see changes and intervene quickly. If contamination does occur, it’s important to be able to trace the contaminant back to the environment to find root cause and prevent it from happening again. Having a robust sampling program and detailed trending will facilitate that investigation. Trending your environmental monitoring data is not just a helpful tool, but it’s also a regulatory expectation. Individual data points become more valuable when you can see the big picture and changes over time.

Microbial identifications are a critical piece of these contamination control strategies. Thus, it’s essential to understand the factors that influence the accuracy of microbial identifications. These include the identification method, how that identification method is executed, data analysis and interpretation, and finally, library coverage. There are a number of different methods that can be used for IDs, and each method has a number of commercial systems. Information in the cell is inherently stored within the DNA, which is then transcribed into mRNA, which is translated into protein by the ribosome. Those proteins are then expressed in a variety of ways. At each point, there is an available identification method. Genotypic IDs are done through DNA sequencing, proteotypic IDs look at protein distribution within the cells, and phenotypic IDs look at protein expression through metabolism and biochemical characteristics. As you move away from where information is stored in the cell’s DNA, out through protein expression, there is a reduction in accuracy and reproducibility for those ID methods.

DNA sequencing is the gold standard for microbial identifications, but what happens when the sample isn’t compatible with Sanger sequencing? Traditional sequencing methods can be limited in what they can offer if samples are not pure or if they cannot be cultured, if they fail to generate usable data, or if the target DNA is large (multiple kilobases or genome-sized) making the traditional methods complex, expensive, and time consuming. In these cases, and in many other scenarios, manufacturers turn to next generation sequencing (NGS).

Next Generation Sequencing for bacterial and fungal identification simultaneously sequences millions of individual DNA fragments from a sample and provides a snapshot of the microbiome at that point in time. When investigating mixed species environments, it provides an understanding of microbial populations without the need for any culturing. Additionally, when studying pure isolates and/or sequencing of mixed species environments, NGS provides a deeper resolution of organism genes and variants at a level never before possible.

There are many applications of NGS for pharmaceutical and consumer care manufacturers. NGS can be used for microbiome analysis of environmental or water system monitoring, microbial cell line characterization or authentication, toxin or virulence gene family detection, contamination detection, plasmid sequencing, resistance gene detection, and probiotic profiling.

Given the importance of clean and effective products, the utmost care must be given to manufacturing and operational excellence. Every tool must be utilized to protect the product and the patient. This includes robust environmental monitoring, high quality and accurate microbial identifications, and the adoption of tools like next generation sequencing.