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What Role Does Microbiology Play in Supporting Drug Development?

Small Molecule Development & Manufacturing at Quotient Sciences

Pharmaceutical products are subject to several rigorous quality controls to guarantee their identity, strength, quality, and purity. In this blog, we will discuss the important role that microbiological quality controls play in the drug development process.

Microbiological quality controls are requirements that have been put in place by global regulatory bodies to prevent the risk of adverse effects to patients. These controls monitor the presence of pathogens and their toxins in the treatments that are administered to patients in order to ensure their safety.

Failing to establish and follow appropriate written procedures designed to avoid microbiological contamination of drug products can cause delays in the development process, out-of-specification occurrences, non-compliance during audits, and, of course, potentially significant safety concerns. Hence, it is vital that these controls are adequately validated for their intended purpose and followed meticulously to ensure compliance with the current Good Manufacturing Practice (cGMP) guidelines for non-sterile and sterile products.

Microbiological quality controls must include but are not limited to:

  • environmental monitoring of the facilities, equipment, materials, and personnel
  • adequate design of testing laboratories and processes
  • establishment of scientifically sound and appropriate specifications, sampling plans, and test procedures to ensure the microbiological quality and the safety of the final product

Microbiological tests are performed throughout the whole drug development process, from the release testing of the active pharmaceutical ingredient (API) and excipients, through to the testing of in-process samples (IPC) and bioburden (the number of microorganisms present in a product/sample), and up to the final drug product release. Risk assessments must be performed for each drug substance and drug product to determine which tests are required for each phase of development according to the source, administration route, manufacturing process, and type of product. Testing programs must be designed to assess the stability of the drugs at specific storage conditions, and the results of these stability tests are used to determine appropriate storage conditions and expiration dates for the product.

The horseshoe crab: the unsung hero of endotoxin testing

If you have been vaccinated, know anyone with a knee replacement, or have received intravenous (IV) antibiotics, you are indebted to the horseshoe crab. Bacterial endotoxin testing is performed on drugs and medical devices that will come in contact with the blood stream using a reagent that comes from the blood of a horseshoe crab. Humans that are exposed to harmful levels of endotoxins can suffer severe illness, so products like vaccines, injectable drugs, IV solutions, and implantable medical devices are quality tested to ensure that they do not contain unsafe levels of endotoxins.


The horseshoe crab has an immune and blood coagulation system that protects it against infections. The horseshoe crab’s blood cells contain proteins that are released in response to the presence of unwanted organisms, such as Gram-negative bacteria (endotoxins are structural components of the Gram-negative bacteria that are released when the cell is destroyed), and cause its blood to clot around the injury and bacteria, protecting the animal from further harm.

In the 1960s, Frederik Bang and Jack Levin developed a test from Limulus polyphemus (Atlantic horseshoe crab) blood that detected the presence of endotoxins. This test, based on the fact that the blood of the horseshoe crab clots when it comes in contact with endotoxins, was called the Limulus amebocyte lysate (LAL) test and was commercialized in the United States in the 1970s. 

The LAL test methods have advanced since the early days, all with the purpose of helping to make injectable drugs, vaccines, and medical devices safer for humans and animals. In addition to the use of their blood for endotoxin testing, the horseshoe crab's DNA has been used to develop a recombinant test method for endotoxins. Even as alternatives are being developed that will retire or reduce the use of horseshoe crab blood, we will always be indebted to the horseshoe crab's contribution to our health.

Manufacturing facilities, like ours at Quotient Sciences, are the first layer of defense to prevent opportunistic microorganisms from colonizing pharmaceutical products that will be reaching patients in the clinic, at home, and at hospitals. Controlling the entry of unwanted microorganisms into pharmaceutical manufacturing facilities and performing validated tests on the products before releasing them significantly reduces the number of outbreaks and product recalls and increases the safety of the treatments. Otherwise, unsuccessful contamination control strategies can cause negative consequences, both economical and human. This approach must be established from the beginning of the drug development process to ensure that the product can be used safely during the clinical trials and must be followed once the product is approved for commercial release.

What is enumeration testing, and why do we have to do it?

For APIs and raw materials, for oral products, and for products before the final sterilization process, it is necessary to quantify the amount and the type of microorganisms present in the product. This is to ensure that the flora in the product is not hazardous, and the levels are within the defined safe limits zone. Not all products must be sterile – for example, some are administrated orally, where the drug must pass through our natural microbial defense system. However, the contamination control strategy is still important to maintain the microbiological quality of products.

To quantify the microorganisms in a product, we use enumeration testing, known as total aerobic microbial count (TAMC) and total yeast and mold count (TYMC). These are quantitative tests that check the number of aerobic microorganisms and the yeasts and molds present in a sample. We use different types of media that are full of nutrients, and we incubate the samples at ideal temperatures for the growth of the microorganisms. If present, microorganisms are visually countable (in colony-forming units) after a determined period of time.


At Quotient Sciences, we employ microbiological testing as part of our integrated Translational Pharmaceutics® programs. Our microbiology laboratories and experienced microbiologists are capable of performing several types of testing to cover all the microbiology needs of our customers under one roof. For non-sterile and sterile drug substances and drug products, a full method development and validation service is offered to support the application of key microbiological techniques. As method development, validation, and testing can all be performed at one facility, there is no need for time-consuming material and technology transfer activities. In addition, we are equipped to perform microbiological testing on radiolabeled, high-potency, and some cytotoxic and controlled substances.

Our microbiologists are not only involved in the testing of the samples, but they are also an integral part of the manufacturing process, including:

  • ensuring the facilities, equipment, materials, and personnel are monitored using settle plates, contact plates, air samples, and swabs
  • performing gowning validation for the personnel working in the classified cleanroom areas
  • assessing aseptic techniques
  • supporting media fill simulations

At Quotient Sciences, our expert team of microbiologists pride themselves on applying their knowledge and skills to ensure that pharmaceutical drug substances and drug products are safe and meet today’s rigorous quality specifications and regulatory standards. To find out more about Quotient Sciences’ microbiology services, take a look at our info sheet.