<img alt="" src="https://secure.inventiveperception365.com/789096.png" style="display:none;">

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

POSTED BY Rapid Micro Biosystems | 13 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 have explored 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. We invite QC labs considering their own evolution from manual plate counts to automation to contact us with any comments or questions.

Best Practice for Security and Control

It is important to design security roles into the software to limit the ability of analysts to modify important configuration settings. For routine tests, analysts ideally should not be able to select from a range of processing methods as errors can occur. Ideally no method selection is required to define the method appropriate for the type of plate/media under test. This assures consistent conduct of testing and simplifies second person review – if the correct process method/version was in use, the equipment configuration is correct.

Digital controls enable enforcement of actions. Security roles determine the actions of each and preserve a record of roles held by personnel so actions can be limited to the minimum number of personnel needed to perform an action, especially enhanced actions that merit closer review such as modifications to original test results or reprocessing plate images to generate new counts.

Another advantage of digital systems is control. Analysts cannot ignore or bypass technical controls enforced by the system, while manual controls such as procedures can be ignored or bypassed. With manual plate counts, analysts can record plate counts on unofficial documents and keep test results they wish to preserve, discarding other values or adjusting them at will. In contrast, automated plate readers can be configured to always save a plate count once the count is complete. Analysts can override (adjust) the count or reprocess the plate image, but a record of these actions is captured in an audit trail with a change reason required as part of the change, so a complete record is maintained at all times during the data lifecycle.

FDA recommends that you restrict the ability to alter specifications, process parameters, data, or manufacturing or testing methods by technical means where possible (e.g., by limiting permissions to change settings or data).1

High Risk Activities: Manual Overrides (Adjustments) and Re-Processing

Automated cell counters bring consistency to plate counting by removing human errors and inconsistency. Changes to counting algorithms can be compared and optimized in a scientific manner prior to implementation. However, microbiologists recognize the periodic need to correct an automated count due to such things as spreading colonies, colonies growing inside other colonies, or filamentous organisms.  

The preservation of plate images at the time of testing opens up a new possibility: reprocessing a plate weeks or months after the plate has been discarded. This permits a qualified microbiologist the opportunity to override (adjust) the automated value by providing a new count and a reason to justify the change. Optionally, the microbiologist could choose to re-process the original plate image using a processing method of their choice. In either situation, the audit trail will capture additional data documentation to support this change to the previous result record.

Along with the technical data captured by the system, it is important to implement a second person review process that gives a detailed look to these atypical activities, as they represent high risk actions to regulators. Reviewers need to assess the changes carefully to assure that not only is the data record complete but is also scientifically justified.

Metadata Is Gold

Data captured by the system can be extracted to perform searches that were not practical in a manual test environment. Date and time stamps represent a treasure of information: for example, start and end times of samples can compute total use time of the system, total analyst time, numbers of batches, or system use by time of day. The number of manual overrides, re-processed plates, results for a specific room, product, sample point, or anything captured about a sample, media or person can be plotted vs plate counts.

Timestamps can be used to verify that activities were performed on correct time intervals consistent with the written procedure, or can prove that a procedure is being followed as written. 

Between September 26 and December 23, 2018, your biological quality laboratory allowed EM and testing plates used for monitoring your facility to be incubated beyond the days established in procedures.2

USP chapter <61> defines incubation parameters for microbiological testing that differ from your procedure.3

Automated Trending

Results stored in a searchable database provide the ability to automate trending and the reporting of potential issues in trending or individual values (OOS). Thus, it is possible to notify management of issues that require a response without dependence on an analyst for notification. Timely notification enables an investigation to reduce the potential impact to product.

Effective Use of Electronic Systems

In addition to validation of the system after configuring it for use, it is equally important to apply data governance to assure that the system and its data remain in a state of control, and the data continues to be accurate and trustworthy. Good data governance includes the following:

  • Data governance policy
  • Procedure for system administration
  • Procedure for system calibration and maintenance
  • Procedure for use of system – includes manual overrides and re-processed plates
  • Procedure for review of electronic records, including critical audit trails (such as overrides and re-processed plates)

Due to their high risk to data integrity and high regulatory exposure, it is recommended that manual overrides and re-processing be reviewed by a senior microbiologist as routine practice. Firms should reasonably expect that these records will be reviewed by inspectors once they learn the system will permit them to be done. Regulators look at these records to assure that these actions were not carried out to accept products that fail to meet specifications (informally known as “testing into compliance”).


During the installation and implementation phases, the need for data archiving should be considered, especially when all plate images and audit trail records must be retained to have a complete record that permits reconstruction of testing. Data should be initially preserved in original format so it can be accessed using the active vendor software/hardware. However, original data intended to be kept for long term (especially 10 or more years) will probably require conversion to an alternate format that can be retrieved by third party software/hardware systems, as analytical instruments typically have lifecycles of less than 10 years. Such conversions may result in loss of some original data, and the risks to the complete (original) test records and the firm’s ability to defend test results that are decades old must be considered and approved prior to any data conversion process. For additional information, see Appendix O1, Retention, Archiving, and Migration in ISPE GAMP Guide: Records and Data Integrity-2017 (available at ispe.org).


Automated plate counting offers unprecedented capabilities: consistent counting, time savings and reduced fatigue for analysts, automated capturing of complete, original data for review, monitoring and trending analysis. Captured plate images permit future examination and re-processing of plates. It also enables the ability to re-process using different configuration settings to compare differences between parameters.

In addition to capabilities, the ability to control access to configuration settings and data through technical controls, automated capture of metadata such as user ID and timestamps, and the elimination of data transcription errors of plate counts all improve data integrity for the process.

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 April 2022 issue of Cleanroom Technology.

Part I  |  Part II  Part III  |  Part IV


1Food 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

2FDA Warning Letter to Pfizer Healthcare Pvt Limited, March 25, 2020. Available at https://www.fda.gov/inspections-compliance-enforcement-and-criminal-investigations/warning-letters/pfizer-healthcare-india-private-limited-594972-03252020

3FDA Warning Letter to Baja Fur S.A. de C.V., December 13, 2019. Available at https://www.fda.gov/inspections-compliance-enforcement-and-criminal- investigations/warning-letters/baja-fur-sa-de-cv-590791-12132019