In non-sterile manufacturing environments, the challenge is to assess which microorganisms are at concern. Should we care only for known pathogens at regulatory board “lists” or should we care about other microorganisms that might cause adulteration concerns among other quality related issues such as color changes, odor issues, phase separation, flocculation, active degradation, among others. Which are the objectionable microorganisms we should care about?
Here are some of the main causes of microbiological contamination in setting initially assessed as robust from the microbial point of view.
- Material: Unqualified shipment and transfer process from supplier to operations
Examples: Liquid Sorbitol bioburden at suppliers (presence of gram-negative), lyophilized flavors with pseudomonads; condensation inside shipment containers nurturing Pseudomonas aeruginosa.
- Unpreserved or poorly preserved aqueous raw materials
Example: Sorbitol liquid material relying in lower water activity promoted by the polyols not effective against a variety of gram-negatives (ie. Acinetobacter, Stenotrophomonas); saline premixes and halophilic risk (ie. Halomonas spp); unpreserved premixes stored and non-monitored (ie. carboximetylcellulose based) or poorly preserved (ie. dye premixes with 15% ethanol; poorly preserved highly vulnerable products (ie. Wet Baby or Facial Wipes) to meet consumer desire for natural products.
- Material transfer pipeline, valves and sampling port do not meet clean design requirements.
Example: Ship trucks with hose ports, valves and hoses not clean design; improvised sampling port at receiving operation with dead leg; transfer line not sanitizable end to end; poorly design drains directly connected to the process; manual touches of operators due to dismantling practices.
- Poor understanding of regular bioburden. Particularly related to the adaptability features of some microorganisms to survive extreme conditions such as low pH, high temperatures, desiccation, salinity, etc.
Example: Halomonas coming from calcium carbonate powder material; Chryseomonas surviving at low pH; Pseudomonas striving at condensation points inside piping, tanks and closed loops maintained at optimum temperatures where bacteria strive (ie. Pseudomonas aeruginosa); assuming no growth will be detected in hot loops (pseudomonas aeruginosa surviving environments at >80 oC); focus only on pathogens and no awareness of objectionable (example, acidophiles as Gluconobacter, acetobacter); Burkholderia Cepacia Complex (BCC) species frequently appearing at water systems and other aqueous systems; powdered dyes as point of entry of microbial contamination (gram-negatives, gram-positive, yeasts and fungi).
- Poor and/or non-validated cleaning processes
Example: not assessing the difficult to clean areas; not using rigorous parameters to verify cleaning; assuming previous strategies for cleaning will be as efficient for the new products and new initiatives (toothpaste with silica vs toothpaste with calcium carbonate); difficult to clean materials as silicone based, encapsulated perfumes used in home care and beauty care products; manual cleaning at fillers that require disassembling /reassembling for cleaning (skin borne contamination); isotainers cleaning process ineffective, stagnated water inside, non-drainable isotainers; flex tubing feeding materials not replaced on regular basis and not sanitized; use of less quality water quality for cleaning compare to the one use for making purposes.
- Non-validated sanitization processes
Example: assuming high temperatures will kill all microorganisms in a piping line not assessing clean design gaps, accumulation points, and other micro risk relevant parameters; not rotating chemical sanitizers, not understanding their limitations; not including drains, transfer hoses, tubing as part of the sanitization practice; lack of verification, not waiting for sanitization results before unloading materials; use of contaminated disinfectant (e.g. Acinetobacter growing in ethanol solution, QUATs with Pseudomonads).
- No establishment of alert and action levels as part of the environmental monitoring or no reacting timely to those levels
Example: vulnerable points or system not included in the environmental monitoring program, focus only on user points (ie. Quarantine tanks at receipt; pretreatment points in water system).
- Poorly qualified human resources at operations, lack of microbiological risk awareness during the day-to-day decisions, operations and change management
- Believing operations can validate long periods of cleaning and sanitization processes without nurturing biofilms
Example: non-clean design tank (cubitainer) storing preserved dye with “validated” C&S frequency periodically extended from 7 days to every 70 days. Involved in a contamination with Enterobacter which appears 1.5 years later.
- Poorly assessed management change
Example: change management team conformed by unexperienced / unqualified local operators or resources unable to see the risks; hose handling; quick repairs impacts; local initiatives in water system affecting other areas of operation; new loop or new user points added to making water system without proper validation.
- Lack of microbiological capability at the site
Example: no site microbiologist, quality manager without microbiology background, unqualified laboratory resources (in site or external), rely only on rapid qualitative methods and no knowing what to do when positive repetitive positive signal obtained.
- Primary packaging (bottles, caps, pouches) is poorly handled, and sources of contamination: yeast, fungi, gram-positives (bacillus and skin-borne), gram-negative in areas subjected to high humidity.
- Manufacturing areas with product making exposed to uncontrolled environment (dirtiness, pests, condensation points)
Example: warehouses transformed into making operations without transition areas, HVAC control, air changing and purification units (filtration), making areas directly in contact with external areas or construction areas; condensation points in drying line, dropping water on top of exposed product considered non-micro vulnerable resulting in contamination with pseudomonads (medicines); expanded fungal contamination due to lack of protection of construction areas and pass-through of materials in making areas (cross-contamination).
- No understanding of the limitations of the methods used for microbiological quality control: accuracy, sensitivity, specificity. Not understanding the associated assumptions.
Example: Low sensitive Total Plate Count method used to test powder raw material, low levels of microorganisms won´t be able to be detected; Suitability testing not executed, not able to demonstrate ability to detect microbial contamination; suitability testing for objectionable microorganisms not executed (blind for some microorganisms); quality control testing conditions not adequate to promote growth of objectionable microorganisms; disregarding importance of low growing microorganisms (e.g. Halomonas, Stenotrophomonas maltophilia in preserved or disinfectant active ingredients matrices).
- Improvisation – Use of temporary non-qualified production lines or facilities to overcome supply chain outages
Example: spray disinfectant temporarily transferred to a contract manufacturing claiming having the capability to produce sprays. Line became rapidly contaminated, and production lost.
- Poorly assessed risk – Use of non-controlled, non-sterile products in highly susceptible consumers ie. Patients in hospitals
Example: shaving cream used in ICU patients causing respiratory infections in some of them. Infection through catheter colonization. Burkholderia vietnamensis involved. 2022.
- Oversight capability of third-party operations (contract manufacturing and external laboratory). Assuming certifications, accreditations and non-conducting auditing at the third partner processes to verify capability on regular basis.
Example: not assessing rigorously the clean design gaps at third partner operations and not requesting validation of their critical processes and risk mitigation strategies; local microbiology laboratory with analyst poorly qualified not able to detect microbial contaminations on time.
- Myths or paradigms – example, no microorganism passes the Reverse Osmosis System; no microbial contamination should be expected from dry low water activity materials or substrates; only spore forming survive to extreme environmental conditions; gram-negatives growing in salt or sugar or sucrose (ex. Ralstonia, Pseudomonas), or in powdered materials coming from mining (ie. Halophytes), high temperature processes (Pseudomonas from lyophilized processes) or natural sources (ie. Pearl powder used in cosmetic applications). Overseeing the highly adaptative features describing most of the microorganisms on Earth.
- Lack of control of the Water treatment process supplying water to manufacturing (water as raw material, process aid or for cleaning and sanitization purposes).
Example: only reacting when water reach out of specification; water system only monitored at point of use; not performing trend analysis on the microbial counts, alert and action levels not established; not understanding the regular bioburden at the water system; not knowing the vulnerability of the different components of the water system; not understanding the limitations of the installed treated systems and components; lack of preventive maintenance; lack of regular upgrades of the system to accommodate to new technologies and new site requirements and needs.
- Powders materials do not handle properly carrying diverse bioburden from gram-negatives, spore-forming bacteria and fungi (yeast and filamentous). Examples: salt, saccharose, sucrose, sugar. From non-qualified suppliers, non-qualified shipping and storage, no filtering, no EPI on operators, non-controlled areas at facilities where the material is exposed to the environment (ie. Silos).
Conclusion
This broad list of causes are just examples showing the challenges faced by non-esterile operations not counting with final esterilization points to deal with remaining bioburden. The key recommendation facing contamination is to always perform a detailed root-cause investigation, critical to fully correct the problem, avoid recurrence and mitigate the risk in the future.
Images inside the picture taken from:
1 taken from ‘Microbiome-friendly’ – What does this label mean in cosmetics? – The Secret Life Of Skin
2 taken from Microbiological Testing – Here2Grow – Cosmetics & Homecare Labs U.K.
3 taken from Pin auf Continuous Improvement (pinterest.com)

Beatriz graduated in Biology in the Universidad Central de Venezuela (UCV), PhSc in Physiology and Biophysics by Instituto Venezolano de Investigaciones Científicas (IVIC) – Caracas, Venezuela; and Postdoc in Biophysics at Univ. of Califórnia (UCLA), Los Angeles (USA).
23+ years of work experience in Industry at Procter & Gamble, having global and regional responsibilities in the areas of Industrial Microbiology (R&D and manufacturing), Open Innovation, and quality assurance. Before P&G. worked also in academy and research during 13 years. Teaching experience (3 years) delivering courses for graduate and post-graduate students at UCV and IVIC.
Currently, delivering services as independent consultant in Quality Assurance, Industrial Microbiology, Open Innovation and Coaching at the BMRV Consulting (https://bmrvconsultoria.com/); active member of the Innovation Commitee of ABIHPEC (Brasilian Association of Industries of higiene, personal care, perfumery and cosmetics), and member of the Global Chamber, among others.