PDA Letter Article

Microbial Control of Raw Materials Used in Pharmaceuticals

by David Jaworski, PDA, Inc.

I hear people say at PDA meetings that nothing ever seems to get resolved. Many PDA members get frustrated when they see the same topics covered at each meeting year after year. One of these topics is microbiological contamination.

When I reviewed recall information from the FDA website, I discovered that there were 37 FDA-documented microbial contamination recalls from 2018 to the present (Table 1) (1). An analysis of FDA enforcement reports from 2012 to 2019 conducted by Luis Jimenez found that 87% of recalls for sterile drugs were associated with unidentified microbial contamination. These recalls included only products that were manufactured and released to the market (2).

The FDA, in their Guidance for Industry: Microbiological Quality Considerations in Non-Sterile Drug Manufacturing, stated that there were 197 adverse event reports associated with intrinsic microbiological or fungal contamination, and 32 of those adverse event reports documented serious adverse patient outcomes between 2014 and 2017. When you look at the true number of drug products that are manufactured and rejected for microbial contamination before they could be distributed, the number of lots where microbial contamination is detected is significantly higher. Other lots of drug products have found microbial enumeration test results that have CFU counts below the drug product’s specification and are released. In these cases, the bacteria present could adapt to the drug formulation and eventually proliferate during storage. Due to the nonuniform distribution of potential microbial contamination, a sample of a drug could have no microbes present but still be contaminated, and these drug products could be released because they met microbial test specifications even though they adversely affect patients’ health when administered. This is true for nonsterile and sterile drug products.

Microbial contamination can lead to drug degradation and result in subpotency. Patients can be exposed to pathogens or opportunistic microorganisms that can cause serious metabolic harm or lead to a patient’s death, especially if the patient is immunocompromised. Other microorganisms can produce harmful microbial toxins that can cause serious patient harm and death.

Microorganisms Associated with Microbial Contamination

Let’s look at some of the microorganisms that have been associated with microbial contamination and are of concern to patient safety.

Burkholderia comprises the majority of microbial contamination found in recalled drug products. The genus Burkholderia contains over 80 formally named species. Only Burkholderia pseudomallei, B. mallei, B. cepacia complex and B. gladioli are generally recognized as human pathogens. These organisms are aerobic, non-spore-forming, nonfermenting Gram-negative bacilli. With the exception of the host-adapted pathogen B. mallei, all are environmental organisms. B. pseudomallei causes melioidosis in both humans and animals and is designated a tier 1 select agent by the U.S. Centers for Disease Control and Prevention (CDC).

  • Poisoning incidents caused by bongkrekic acid (BA), one of the metabolites of the Burkholderia gladioli pathovar cocovenenans (B. cocovenenans), have been reported in Indonesia, Mozambique and China. It is an odorless, tasteless heat-stable polyketide. A lethal dose of BA — between 1 mg/kg and 3.16 mg/kg — can kill within 1–10 hours after exposure.
  • Bacillus cereus is associated mainly with food poisoning and serious eye infections but can cause a serious and sometimes fatal infection that produces tissue destructive exoenzymes and toxins. It is a deadly nosocomial infection that is taken seriously in hospitals (3).
  • Pseudomonas fluorescens can cause bacteremia infections and has been associated with Crohn’s disease (4).
  • Ralstonia pickettii is a persistent Gram-negative nosocomial infectious organism that takes advantage of underlying patient conditions and diseases (5).
  • Gluconacetobacter liquefaciens is a Gram-negative plant pathogen that has only been associated with infection of immunocompromised patients (6).

These are just a few examples of where microbial contamination can have a serious effect on patients. You may think that Burkholderia would not survive processing of raw material or that BA contamination is not a problem, but many of the raw materials used to manufacture drugs are manufactured in Asia and India. Could Burkholderia or potent toxins be present in the raw materials you purchase and use to manufacture drug products?

Many microbial contamination events can be traced to in-process contamination events during drug product manufacturing, but that is not the entire story. For example, Klebsiella oxytoca, commonly found in biofilms, was found in a process stream after a column-purification step. Isolates of this organism were found to produce a cytotoxin, so an API lot was rejected. In another incident, there were docusate sodium oral solution lots contaminated with B. cepacia that were linked directly to a contaminated process-water system.

Microbial contamination control programs have been around since 1969, when NASA published their Handbook for Contamination Control on the Apollo Program (7). In 2001, Sandra Lowery wrote a chapter on designing a contamination control program for Richard Prince’s 2001 book, Microbiology in Pharmaceutical Manufacturing, Vol I. In this chapter, only one page out of 62 pages mentioned bioburden of raw materials, which can be a source for many contamination events observed (8). So, where have drug manufacturers gone wrong?

The main sources of microbial contamination of drug products are:

  • Raw materials and components
  • Lack of effective cleaning and in-process controls
  • Humans
  • Container closure system failures
  • Sterilization failures

Raw Material and Component Contamination

The remainder of this article will focus on raw materials and component contamination. Future articles will address the other sources of microbial contamination.

Many of the buyers I have dealt with over the years have stated that there is no need for microbiological controls for the APIs and excipients used to make drugs because they go through chemical processing. The same argument is made for components, cleaning materials and other ancillary manufacturing supplies needed for drug manufacturing, as if some miracle happens and microbes are not present on these purchased items. In my experience, these assumptions are not based on reality; they are most likely based on the goal of lowering material costs.

Many APIs and excipients truly are chemicals that do not support microbial growth, but there are a host of other APIs and excipients that will support microbial growth under the right conditions. Naturally sourced materials, such as plant extracts, can be found to contain high levels of bacteria, molds and yeast upon testing. Fermentation products also can contain microbial toxins and metabolic contaminants if not controlled properly.

APIs and excipients come via long supply chains where contamination can be introduced by using improperly cleaned containers, through inferior containers that do not properly protect the content of the materials, or during transportation and storage. Additional transportation-related concerns include moisture from rain at an airport ramp or leaking warehouse roofs, vermin contamination or containers damaged during handling.

In many cases, API and excipient manufacturers do not think that sanitation and environmental controls are needed since they are not making a sterile product. I have seen very poor manufacturing conditions at some chemical processing facilities, especially in countries that do not practice strong hygiene principles.

Water is another source of microbial contamination. Water is used throughout many raw-material and drug-product manufacturing processes and can be a significant ingredient by itself in many injectable and oral drugs.

With so many sources of raw materials and ingredients coming from different countries, different companies and various manufacturing processes, there is a need for effective microbial contamination control strategies. That applies to the raw materials, ingredients and manufacturing aids used to manufacture drug products.

The following contamination control strategies have been proven effective and are recommended for implementation by the manufacturers of the raw materials:

  • Design of manufacturing processes that minimize microbial contamination
  • Microbial risk assessment of raw materials and ingredients
  • Development of effective audit checklists for suppliers focused on microbial control
  • In-person audits of manufacturers
  • Supplier quality agreements established with a focus on microbial control
  • Control of storage conditions in warehouses and during transit
  • Control of processing times
  • Effective maintenance of facilities and equipment
  • Effective cleaning of equipment and facilities
  • Minimization of contact with humans
  • Control of vermin and insects
  • Control of containers used to store and ship materials
  • Control of supply chain
  • Control of water systems
  • Control of wastewater and waste
  • Development of pasteurization or sterilization processes for natural ingredients
  • Development of microbial test methods and specifications based on risk assessments
  • Effective investigation of microbial contamination of drug products

Useful Resources

Risk assessment is one of the key tools that can be utilized by a raw material manufacturer or drug product manufacturer to ensure that the materials used to manufacture a drug product do not have excessive levels of microbial or endotoxin contamination. PDA Technical Report No. 44: Quality Risk Management for Aseptic Processes is an excellent resource that can be used to perform risk assessments of manufacturing processes and raw material sources. Beyond this resource, it is very important that company personnel have the proper training and expertise to perform effective risk assessments. There is always the chance that people performing risk assessments will minimize the risk of microbial contamination that can be present in the raw materials, APIs and excipients used in drug product manufacturing. To overcome these biases, PDA Technical Report No. 67: Exclusion of Objectionable Microorganisms from Nonsterile Pharmaceuticals, Medical Devices, and Cosmetics is a good primer on the evaluation of microbial risks and the steps needed to control microbial contamination sources.

Effective environmental control is another important aspect of raw material and excipient manufacturing that has a direct impact on the materials being manufactured. In one case, a manufacturer of an API had a closed-process stream used to manufacture the API, but the process equipment was exposed to outside conditions that allowed birds to roost in the ceiling areas above the process equipment. During maintenance of the equipment train, some of the bird feces entered the process piping and contaminated the interior of the equipment, which led to multiple lots of the API having high levels of microbial contamination. Section 4.3, “Environmental Controls,” in PDA Technical Report No. 54-4: Implementation of Quality Risk Management for Pharmaceutical and Biotechnology Manufacturing Operations, discusses a model for environmental control design that can be effectively used by raw-material and excipient manufacturers to control the chance of environmental microbial contamination.

A comprehensive cleaning program should be designed to ensure cross-contamination is controlled, degradants are removed, bioburden is controlled and endotoxins have not accumulated in the manufacturing equipment trains and facilities used to produce raw materials. An excellent resource on comprehensive cleaning is PDA Technical Report 29 (Revised 2012): Points to Consider for Cleaning Validation. It provides a scientific approach to the design of cleaning processes, how the processes can be assessed, and help in determining the correct approach to cleaning in general.

When you do find microbial contamination in a drug product, it is very important that you are prepared to conduct an extensive investigation to determine the cause of the contamination. The root cause of microbial contamination is very hard to determine in some cases, and a scientific investigation is the best method to use. “Case Study 4: Melamine Contamination (Supply Chain)” in PDA Technical Report No. 54-3: Implementation of Quality Risk Management for Pharmaceutical and Biotechnology Manufacturing Operations, Annex 2, provides an example of a chemical contamination event. It discusses how the effective use of Failure Mode Effect Analysis can help determine the root cause and risk areas to investigate. This same methodology can be used for microbial contamination investigations.

When you detect a microbial contamination event in a drug product based on microbial testing, there is a comprehensive investigation process in PDA Technical Report No. 88: Microbial Data Deviation Investigations in the Pharmaceutical Industry that can be followed. Section 5.0 on “Phase II: Manufacturing Investigation” is very useful in helping raw-material and excipient manufacturers address a microbial contamination deviation reported by a drug product manufacturer that could implicate its supplied materials.

Bioburden generation and biofilm formation are major sources of microbial contamination in bulk drug substance manufacturing and process water systems. There is an excellent bioburden management program discussed in PDA Technical Report No. 69: Bioburden and Biofilm Management in Pharmaceutical Manufacturing Operations that raw-material and excipient manufacturers can utilize to prevent or control these sources of microbial contamination.


The recall and enforcement facts identify that significant microbial contaminations of drug products remain an issue for the industry. Effective microbial contamination control measures exist and need to be applied to the raw materials and APIs used to make drug products. Much of the information on microbial control is based upon common-sense approaches to prevent microbial contamination, which is an ever-present challenge to materials used in manufacturing drug products.

For Further Reading

Additional sources of information can be found in the guidances for industry from the International Council for Harmonisation (ICH) Quality Guidelines Q6A, Q6B, Q7A, Q9 and Q10, which are recognized by both the European Medicines Association and U.S. FDA (9). Although not directly attributable to excipients, gases and water, the recommendations in these guidance documents can also be applied to those ingredients. Risk assessment information can be found in PDA Technical Report No. 54-6: Formalized Risk Assessment for Excipients.


  1. U.S. Food and Drug Administration, “Recalls, Market Withdrawals & Safety Alerts.” https://www.fda.gov/safety/recalls-market-withdrawals-safety-alerts (accessed 9 Jul 2022).
  2. Jimenez, Luis. “Analysis of FDA Enforcement Reports (2012–2019) to determine the Microbial Diversity in Contaminated Non-Sterile and Sterile Drugs.” American Pharmaceutical Review, Oct 24, 2019.
  3. Bottone, Edward J. “Bacillus cereus, A Volatile Human Pathogen.” Clin Microbial Rev., 2010 Apr; 23(2): 382-398. doi: 10.1128/CMR.00073-09.
  4. Scales, Brittan S., et al. “Microbiology, Genomics, and Clinical Significance of the Pseudomonas Fluorescens Species Complex, an Unappreciated Colonizer of Humans.” Clin Microbial Rev., 2014 Oct;27(4): 927-948.
  5. Ryan, M.P., et al. “Ralstonia pickettii: a persistent gram-negative nosocomial infectious organism.” J Hosp Infect. 2006 Mar; 62(3): 278-84. doi: 10.1016/j.jhin.2005.08.015.
  6. Maxwell Olenski et al., “A Case of Gluconacetobacter liquefaciens Bacteremia Associated with Sugarcane Juice Ingestion.” Journal of Microbiology and Infectious Diseases. 2020 Mar; 10 (01): 62-67. doi:10.5799/jmid.700538.
  7. Sandia Laboratories, Contamination Control Handbook. Washington, DC: Technology Utilization Division, National Aeronautics and Space Administration, 1969.
  8. Lowery, Sandra A. “Designing and Validating a Contamination Control Program.” In Microbiology in Pharmaceutical Manufacturing, First Edition, edited by Richard Prince, 203-266. Bethesda, Md: PDA/DHI, 2001.
  9. International Council for Harmonisation (ICH), “Quality Guidelines.” https://www.ich.org/page/quality-guidelines (accessed 9 Jul 2022).
Table 1 FDA Microbial Contamination Recalls, February 2018 to September 2022
Date Brand Names Product Description Recall Reason/Description Company Name
02/06/2018 Centurion Ninjacof and Ninjacof A Potential contamination with Burkholderia cepacia Centurion Labs
02/08/2018 Doctor Manzanilla Allergy, cough medicine Burkholderia cepacia Mid Valley Pharmaceutical
02/08/2018 Leader, Major, Rugby Diocto Liquid and Diocto Syrup Potential contamination with Burkholderia cepacia Cardinal Health
07/20/2018 Dr. King’s, Dr. King’s Aquaflora Homeopathic liquids: Candida liquid, lymph detox liquid, baby teething liquid Microbial contaminants Pseudomonas Brenneri, Pseudomonas Fluorescens and Burkholderia Multivorans King Bio Inc.
05/24/2019 La Bella Extreme Sport Styling Gel Bacterial Contamination (Burkholderia cepacia and group of related strains) The Village Company
08/15/2019 RELPAX RELPAX® (eletriptan hydrobromide) 40 mg tablets Microbiological Contamination Pfizer Inc
09/26/2019 LemonPrep Skin prepping lotion for enhancement of signal quality at electrode site Burkholderia cepacia Mavidon
01/08/2020 LemonPrep®, PediaPrep®, Wave Prep, Cardio Prep LemonPrep®, PediaPrep® and Wave Prep 4-ounce tubes and single-use cups, Cardio Prep single-use cups, and all lots of Collodions and Collodion removers Burkholderia cepacia Mavidon
03/19/2020 Neuroveen, Respitrol, Thyroveev, Compulsin Homeopathic Medicines Due to Possible Microbial Contamination Mavidon
03/31/2020 Medline Remedy Essentials No Rinse Cleansing foam Multistate outbreak of B. cepacia complex Shadow Holdings dba Bocchi Laboratories
10/28/2020 Paroex Chlorhexidine Gluconate Oral Rinse, 4 oz and 16 oz Potential contamination with Burkholderia lata Sunstar Americas, Inc.
11/09/2020 Lohxa Chlorhexidine Gluconate Oral Rinse USP, 0.12% Alcohol free May be contaminated with Burkholderia lata Lohxa, LLC
12/02/2020 MPM Medical Regenecare HA Topical Anesthetic Hydrogel Burkholderia cepacia contamination MPM Medical, LLC
12/28/2020 Paroex Chlorhexidine Gluconate Oral Rinse, 4 oz and 16 oz Potential contamination with Burkholderia lata Sunstar Americas, Inc.
12/28/2020 Paroex Chlorhexidine Gluconate Oral Rinse, 4 oz and 16 oz Potential contamination with Burkholderia lata Sunstar Americas, Inc.
12/31/2020 GUM Paroex Chlorhexidine Gluconate Oral Rinse, 15 mL unit dose cups Potential contamination with Burkholderia lata Precision Dose Inc.
03/24/2021 Durisan Antimicrobial Hand Sanitizer Due to microbial contamination Sanit Technologies LLC d/b/a Durisan
04/16/2021 Durisan Hand Sanitizer Product is contaminated with Burkholderia contaminans Sanit Technologies LLC d/b/a Durisan
05/17/2021 Durisan Hand Sanitizer Product is contaminated with Burkholderia contaminans Sanit Technologies LLC d/b/a Durisan
06/22/2021 Durisan Hand Sanitizer and handsanitizing wipes Microbial contamination Sanit Technologies LLC d/b/a Durisan
08/04/2021 Multiple brand names Ultrasound Gel Product is contaminated with bacteria (Burkholderia cepacia complex) Eco-Med Pharmaceutical
9/15/21 Ruzurgi, 10mg tablets tablets Yeast, mold, and aerobic bacteria Jacobus Pharmaceutical
11/10/21 liquid probiotics liquid Pseudomonas aeruginosa Mary Ruth's
12/31/21 Clobetasol Propionate Ointment USP 0.05% ointment Ralstonia pickettii Taro Pharmaceuticals
01/28/22 RevitaDerm wound care gel ointment Bacillus cereus Blaine Labs
3/21/22 Jergens Ultra Healing Moisturizer cream Pluralibacter gergoviae Kao USA
3/30/22 Milk of Magnesia Oral Suspension liquid Microbial contamination Plastikon Healthcare
5/10/22 SyrSpend SF Cherry liquid Burkholderia gladioli Fagron
6/8/22 Allergy Bee Gone for kids nasal swabs Yeast & mold and may contain the bacteria Bacillus cereus Buzzagogo
6/10/22 SnoreStop NasoSpray liquid Providencia rettgeri Green Pharmaceuticals
6/10/22 Milk of Magnesia Oral Suspension liquid Microbial contamination Pastikon Healthcare
6/24/22 Magnesium Citrate Saline Laxative Oral solution liquid Gluconacetobacter liquefaciens Vi-Jon Mfg. for CVS
8/05/22 Magnesium Hydroxide/aluminum hydroxide/simethicone liquid Microbial contamination Pastikon Healthcare

About the Author

David JaworskiDavid Jaworski is PDA’s Sr. Advisor for Scientific Affairs. He was a Senior Policy Advisor at U.S. Food and Drug Administration for more than seven years and had previously worked in the CDER Office of Compliance as a Consumer Safety Officer and as Acting Branch Chief in the Domestic Case Branch. His experience in the pharmaceutical industry encompasses 22 years in business management, research, manufacturing and consulting.