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Strengthening a Weak Link in QC Microbial Testing (Part I)

POSTED BY Rapid Micro Biosystems | 11 minute read

By Mark Newton and David L. Jones

Microbial enumeration testing in the pharmaceutical QC lab is based around well proven traditional manual methods that have changed little since the creation of the first pharmacopeia. These manual processes rely heavily on the training, expertise and judgment of the individuals who perform them. Improvements have been made to the processes to minimize variation such as: use of commercial media, validated incubators, verification signatures and electronic batch records; however, the ability to accurately see and enumerate colonies, then accurately record the information to paper or electronic system, is still a weak link in the forensic data trail.

In this four-part series, we will explore the unprecedented capabilities of automated plate counting: consistent counting, time savings and reduced fatigue for analysts, and automated capturing of complete, original data for review, monitoring and trending analysis. Along the way, we will also suggest key considerations for QC labs evolving from manual plate counts to automation.

Data Integrity and Regulatory Game Change

Microbial enumeration remains one of the few quality control processes where sample collection, processing and result collection, followed by disposal of the final raw data, can be performed without supervision or traceability. Added to this are the pressures on staff to turnaround results quickly that are in compliance. All factors add to create two high risk scenarios for integrity of records: (1) the preparation and transport of samples; and (2) the incubation, enumeration/data transfer stage. The latter portion is concerned with the integrity of the data for discussion in this paper and the “ease to audit the process” from a reviewer/auditor viewpoint.

Platco and Cundell discuss a number of data integrity issues that might occur within the microbiological laboratory1, noting the historically manual operations and their attendant risks of recording and arithmetic errors, including the difficulty in detecting these errors due to data review after the events occur. Until recently, microbiological methods have seldom been implemented using automated technologies.

Although 21 CFR 211.194 (a)(8) requires original records to be reviewed for “accuracy, completeness, and compliance with established standards,” deficiencies in the current (historic) state of manual microbiological methods have been exposed with the enhanced focus on data integrity by regulators in the past decade. De La Torre3 and Unger2 both note the increase in data integrity-related observations, especially since 2015. Between 2015-2018, data integrity issues were present in 70-90% of FDA Warning Letters.3 Data Integrity focused guidance documents from MHRA4 and FDA5 among other regulatory bodies, emphasize the importance of understanding process risks and mitigating them to acceptable levels. Manual processes are difficult to mitigate, because they require people to follow them and leave little evidence of non-compliance to be discovered after the fact.

Platco and Cundell provide a list of risks in the microbiological lab, applicable to most compendial tests performed. In their opinion, the microbial tests at greatest risk for data integrity issues are: “sterility test, the gel clot Limulus Amebocyte Lysate (LAL) bacterial endotoxin assay and any microbial enumeration test which involves counting microbial colonies which covers most of the other compendial tests.”1

Data Integrity Process Risks in the Microbiological Lab1

High Risk

Analyst records incorrect data
No second opinion for subjective interpretation of test results
Analyst performs wrong method or wrong sample preparation
Missed critical data or incorrect information
Falsification or lack of authentic data

Medium Risk

Real time data entry difficulties
Incomplete data entries
Chain of custody for samples issues
Delay in testing, times not documented

Low Risk

Improper recording of non-critical data
Lack of real time entry of non-critical data (lot numbers, expiry dates, and recalibration dates)

PDA Technical Report 806 provides a number of data integrity observations including sampling, sample containers and pre-test storage, excessive use of disinfectants, inaccurate sampling due to inadequate equipment maintenance and calibration. They recommend that plates be retained after counting to permit second person verification to rule out data integrity issues.7

Regulators will continue to examine laboratory operations and data closely, to assure that reported test values are accurate, complete and trustworthy. Assuring that processes are followed requires an additional level of review than has previously been applied to manual processes. This additional review adds additional demands on senior microbiologists and adds time to the release process.

Current State: Microbial Plate Counts

In addition to the data integrity risks of manual techniques, hours at a laboratory bench can create user fatigue resulting in reduced accuracy, requiring analyst breaks. Fatigue can be reduced by adding additional analysts, but this requires significant time investments in training and on-going effort by all analysts to be consistent. Sandle reported the result of a study where two analysts differed in counts by as much as 50% when counting beads in agar to represent colonies.8 Additionally, he describes other factors that influence an analyst’s ability to effectively count plates, including plate position, type and direction of lighting.

Also, plate count results can only be retained and second person reviewed for few hours, after which total counts may change due to appearance of slow-growing organisms, spreading organisms or contamination from the plate reading process. In the past, it was common for lab personnel to review the documentation of plate counts and not the plates themselves, choosing to accept the risk of inaccurate counts. Due to data integrity concerns and regulatory citations of inaccurate plate counts,9 labs must now implement second person review of all plates or find alternate technologies to conduct the methods.

In addition to time limitations for original sample retention, contemporaneous time stamps for start/end of each count permit reviewers to determine if sufficient time was permitted for an accurate colony count but are seldom recorded in manual counts.

Your firm also stated that, after implementing extra plate-reading oversight in the microbiology laboratory, a notable increase in counts emerged in environmental monitoring results, with a particularly “sharp” increase in personnel monitoring excursions across the facility.9

Today’s automated plate counting technologies, in contrast, offer unprecedented capabilities to improve consistency, save time, reduce analyst fatigue, capture data automatically and fully intact, and control reviewer access with unerring documentation – in short, offering myriad ways to satisfy the stringent data integrity standards now driving the pharmaceutical industry.

In the next post of our four-part series, we will address the advantages of digitalization in microbial QC testing. Look for it soon!

Mark Newton is an associate senior quality assurance consultant at Eli Lilly and Company. David L. Jones is director of marketing and industry affairs at Rapid Micro Biosystems. This content previously appeared in edited form in the March 2022 issue of Cleanroom Technology.

Part I  |  Part II  |  Part III  |  Part IV


1Platco, C. Cundell, T. Data Integrity Issues in Microbial Testing, Am. Pharm. Rev, Sept, 2017

2Unger, Barb. FDA FY2020 Drug Inspection Observations And Trends. Pharmaceutical Online, Dec 9 2020. FDA FY2020 Drug Inspection Observations and Trends (pharmaceuticalonline.com)

3De La Torre, Michelle. Data Integrity Trends in 483s and Warning Letters: Part 1. May 16, 2019. Available from Redica.com

4Medicines & Healthcare products Regulatory Agency (MHRA). “GXP Data Integrity Guidance and Definitions.” March 2018. https://www.gov.uk/government/publications/guidance-on-gxp-data-integrity

5Food and Drug Administration (FDA). Data Integrity and Compliance With Drug cGMP: Questions and Answers. Guidance for Industry. December 2018. https://www.fda.gov/media/119267/download

6PDA Technical Report 80. Data Integrity Management Systems for Pharmaceutical Laboratories. 2018. Parenteral Drug Association, Inc.

7PDA TR80 above, Section 5.1.2, pg 12

8Sandle, Tim. Ready for the Count? Back to Basics Review of Microbial Colony Counting. February 2020. Research Gate: https://www.researchgate.net/publication/339416178_Ready_for_The_Count_Back-To- Basics_Review_Of_Microbial_Colony_Counting

9FDA Warning Letter to Hospira Healthcare India Pvt Ltd, March 4, 2019. Available at: https://www.fda.gov/inspections-compliance-enforcement-and-criminal- investigations/warning-letters/hospira-healthcare-india-pvt-ltd-557890-03042019