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〈 1117 〉 MICROBIOLOGICAL BEST LABORATORY PRACTICES

INTRODUCTION
Good laboratory practices in a microbiology laboratory consist of activities that depend on several principles: aseptic technique,
control of media, control of test strains, operation and control of equipment, diligent recording and evaluation of data, and training of
the laboratory staff. Because of the inherent risk of variability in microbiology data, reliability and reproducibility are dependent on the
use of accepted methods and adherence to good laboratory practices.

MEDIA PREPARATION AND QUALITY CONTROL

Media Preparation
Culture media are the basis for most microbiological tests. Safeguarding the quality of the media is therefore critical to the
success of the microbiology laboratory. Media preparation, proper storage, and quality control testing can ensure a consistent supply
of high-quality media.
It is important to choose the correct media or components in making media based on the use of accepted sources or references
for formulas. The manufacturer's formula and instructions for preparation routinely accompany dehydrated media and ready-made
media. Because different media types may have different preparation requirements (e.g., heating, additives, and pH adjustment), it is

〈1251〉〉). Clean weighing

Cleaning Glass
Apparatus 〈1051〉〉

The effects of the sterilization method and conditions on the media should be validated by sterility and growth-promotion testing
of the media. In addition, if sterilized by moist heat, the autoclave cycle should be validated to ensure proper heat distribution for
selected loads and volumes. Typically, manufacturers recommend using an autoclave cycle of 121° for 15 minutes using a validated
autoclave. These conditions apply to time at temperature of the media. As container size and the load configuration of the autoclave
will influence the rate of heating, longer cycles may be required for larger loads. However, the sterilization time will be dependent on
the media volume and autoclave load. Sterilization cycles in which the autoclave is slow to come up to temperature may result in
overheating of the media. Therefore, care must be taken to validate a sterilization cycle, balancing the need for sterile media against
the tendency of the media to degrade under excessive heating. Storage of the media in the autoclave after the liquid cycle is
completed is not recommended after cooling, as it may damage the media. Improper heating or sterilizing conditions—for
commercially prepared or internally prepared media—may result in a difference in color change, loss of clarity, altered gel strength, or
pH drift from the manufacturer's recommended range, as well as reduced growth-promotion activity and/or selectivity.
The pH of each batch of medium should be confirmed after it has cooled to room temperature (20°–25°) by aseptically
withdrawing a sample for testing. Refrigerated purchased media should be allowed to warm up to ambient room temperature if it is
to be checked for pH confirmation. A flat pH probe is recommended for agar surfaces, and an immersion probe is recommended for
liquids. See pH 〈791〉〉 for guidance with pH measurement and instrument calibration. The pH of media should be in a range of ±0.2 of
the value indicated by the manufacturer, unless a wider range is acceptable by the validated method.

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Prepared media should be checked by appropriate inspection of plates and tubes for the following:
• Cracked containers or lids
• Unequal filling of containers
• Dehydration resulting in cracks or dimpled surfaces on solid medium
• Hemolysis
• Excessive darkening or color change
• Crystal formation from possible freezing
• Excessive number of bubbles
• Microbial contamination
• Status of redox indicators (if appropriate)
• Lot number and expiration date checked and recorded
• Sterility of the media
• Cleanliness of plates (lid should not stick to dish)

Media Storage
It is prudent to consider how the manufacturer or supplier transports and stores media before distribution to the end user.
Manufacturers of media should use transport and storage conditions that minimize the loss of moisture, control the temperature,
prevent microbial contamination, and provide mechanical protection to the prepared media.
Media should be labeled properly with batch or lot numbers, preparation and expiration dates, and media identification. Media
should be stored according to the manufacturer's instructions. Media prepared in house should be stored under validated conditions.
Do not store agar at or below 0°, as freezing could damage the gel structure. Protect stored media from exposure to light and
excessive temperature. Before prolonged storage, agar plates should be placed into a sealed package or container to retard moisture
loss.
Remelting of an original container of solid media should be performed only once to avoid media whose quality is compromised by

environmental isolates (but these latter are not to be construed as compendial requirements).
Expiration dates on media should have supporting growth-promotion testing to indicate that the performance of the media still
meets acceptance criteria up to and including the expiration date. The length of shelf life of a batch of media will depend on the
stability of the ingredients and formulation under specified conditions, as well as the type of container and closure.
When a batch of media does not meet the requirements of growth-promotion testing, an investigation should be initiated to
identify the cause. This investigation should include a corrective action plan to prevent the recurrence of the problem. Any batch of
media that fails growth-promotion testing is unsuitable for use. [NOTE—Failed growth-promotion test results may not be used to
negate positive test results.]
Some reagents are used for diagnostic purposes to help support identification of microbial organisms, e.g., Gram stain and
oxidase test reagents. These may have attributes that can be quality control tested similar to microbiological media. Select the
correct quality control standard microorganisms, following the manufacturer's instructions, and perform the testing before unknown
sample diagnostic testing. All relevant diagnostic reagents should be subjected to incoming quality confirmation before use.
Special care should be taken with media that is used in sterility tests (see Sterility Tests 〈71〉〉 for requirements) and in
environmental monitoring studies. Media used for environmental monitoring of critical areas should preferably be double-wrapped
and terminally sterilized. If terminal sterilization is not performed, media should be subjected to 100% pre-incubation and inspection
before use within a critical area. [NOTE—Growth-promotion testing for this media must be performed after the pre-incubation stage.]

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This will prevent extraneous contamination from being carried into controlled environments and will prevent false-positive results. A
raised agar level for surface contact plates should be verified.

MAINTENANCE OF MICROBIOLOGICAL CULTURES

Biological specimens can be the most delicate standards to handle because their viability and characteristics are dependent on
adequate handling and storage. Standardizing the handling and storage of cultures by the user laboratory should be done in a way
that will minimize the opportunity for contamination or alteration of growth characteristics. The careful and consistent treatment of
stock cultures is critically important to the consistency of microbiological test results. Cultures for use in compendial tests should be
acquired from a national culture collection or a qualified secondary supplier. They can be acquired frozen, freeze-dried, on slants, or
in ready-to-use forms. Confirmation of the purity of the culture and the identity of the culture should be performed before its use in
quality control testing. Ready-to-use cultures should be subjected to incoming testing for purity and identity before use. The
confirmation of identity for commonly used laboratory strains should ideally be done at the level of genus and species.
Preparation and resuscitation of cultures should follow the instructions of the supplier or a validated, established method. The
“Seed-Lot” technique is recommended for storage of stock cultures.
The original sample from the national culture collection or a qualified secondary supplier is resuscitated and grown in an
appropriate medium. Aliquots of this stock culture (the first transfer or passage) are suspended in a cryoprotective medium,
transferred to vials, and frozen at –30° or below, until use. If stored at –70°, or in lyophilized form, strains may be kept indefinitely.
These frozen stocks can then be used to inoculate monthly or weekly working cultures. Once opened, do not refreeze unused cell
suspensions after culturing a working suspension. The unused portion should be discarded to minimize the risk of loss of viability
and contamination of the stock.
The number of transfers of working control cultures should be tracked to prevent excessive subculturing that increases the risk of
phenotypic alteration or mutation. The number of transfers allowable for specific compendial tests may be specified in that test. One
passage is defined as the transfer of organisms from a viable culture to a fresh medium with growth of the microorganisms. Any
form of subculturing is considered to be a transfer/passage.

that microbiological samples be handled in an environment that makes contamination highly unlikely.
In general, a laboratory should be divided into clean or aseptic areas and live culture areas. Areas in which environmental or sterile
product samples are handled and incubated should be maintained completely free of live cultures, if possible. If complete separation
of live and clean culture zones cannot be accomplished, then other barriers and aseptic practices should be employed to reduce the
likelihood of accidental contamination. These barriers include protective clothing, sanitization and disinfection procedures, and
biological safety cabinets designated for clean or aseptic operations only. Procedures for handling spills or mishaps with live
cultures should be in place, and all relevant technical personnel should be trained regarding these methods.
Some samples will demonstrate microbial growth and require further laboratory analysis to identify the contaminants. When
growth is detected, the sample should be taken from the clean section of the laboratory to the live culture section without undue
delay. Subculturing, staining, microbial identification, or other investigational operations should be undertaken in the live culture
section of the laboratory. If possible, any sample found to contain growing colonies should not be opened in the clean zone of the
laboratory. Careful segregation of contaminated samples and materials will reduce false-positive results.
Staff engaged in sampling activities should not enter or work in the live culture handling section of a laboratory unless special
precautions are taken, including wearing protective clothing and gloves and careful sanitizing of hands upon exiting. Ideally, staff
assigned to sampling activities, particularly those in support of aseptic processing, should not work in the vicinity of live culture
laboratory operations.

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It is important to consider that microbial contamination of samples, which leads to false-positive results, is always possible unless
careful aseptic precautions are taken. Facilities should be designed so that raw material and excipient sampling can be done under
controlled conditions, including proper gowning and sterilized sampling equipment. It may not always be possible to sample utility
systems, such as water systems, under full aseptic conditions; however, it should be noted that when samples are not taken
aseptically, their reliability is inevitably compromised.
Environmental sampling methods should require minimal aseptic handling in loading and unloading sampling instruments.
Whenever possible, sampling equipment should be loaded with its microbiological recovery media in the environment that is to be
sampled.
All testing in laboratories used for critical testing procedures, such as sterility testing of final dosage forms, bulk product, seed
cultures for biological production, or cell cultures used in biological production, should be performed under controlled conditions.
Isolator technology is also appropriate for critical, sterile microbiological testing. Isolators have been shown to have lower levels of
environmental contamination than manned clean rooms, and therefore, are generally less likely to produce false-positive results.
Proper validation of isolators is critical both to ensure environmental integrity and to prevent the possibility of false-negative results
as a result of chemical disinfection of materials brought into or used within isolators (see Sterility Testing—Validation of Isolator
Systems 〈1208〉〉).

SAMPLE HANDLING
Viable microorganisms in most microbiology samples, particularly water, environmental monitoring and bioburden samples, are
sensitive to handling and storage conditions. Critical parameters in these conditions include product (or sample) composition,
container composition, time of storage, and temperature of storage. Therefore, it is important to minimize the amount of time
between the sampling event and the initiation of testing and to control, as much as possible, the conditions of storage. If the sample
is to be transported to a distant location for testing, then the conditions of transport (time, temperature, etc.) should be qualified as
suitable for that test and sample. Guidance for water testing in this regard can be found in Water for Pharmaceutical Purposes
〈1231〉〉. Product mixing before sampling may need to be evaluated and applied in order to ensure microbial dispersement and

level of skill and experience.

accurate and reproducible results, and so serve as the basis for training. Secondly, by tracking the procedures in which a particular
microbiologist has demonstrated proficiency, the procedure number or title also serves to identify what training the microbiologist
has received specific to his or her job function.
Training curricula should be established for each laboratory staff member specific to his or her job function. He or she should not
independently conduct a microbial test until qualified to run the test. Training records should be current, documenting the
microbiologist's training in the current revision to the particular SOP.
Periodic performance assessment is a wise investment in data quality. This performance testing should provide evidence of
competency in core activities of the microbiology laboratory such as hygiene, plating, aseptic technique, documentation, and others
as suggested by the microbiologist's job function.
Microbiologists with supervisory or managerial responsibilities should have appropriate education and in-house training in
supervisory skills, laboratory safety, scheduling, budgeting, investigational skills, technical report writing, relevant SOPs, and other
critical aspects of the company's processes as suggested in their role of directing a laboratory function.
Competency may be demonstrated by specific course work, relevant experience, and routinely engaging in relevant continuing
education. Achieving certification through an accredited body is also a desirable credential. Further, it is expected that laboratory
supervisors and managers have a demonstrated level of competence in microbiology at least as high as those they supervise.
Expertise in microbiology can be achieved by a variety of routes in addition to academic course work and accreditation. Each

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company is expected to evaluate the credentials of those responsible for designing, implementing, and operating the microbiology
program. Companies can thus ensure that those responsible for the program understand the basic principles of microbiology, can
interpret guidelines and regulations based on good science, and have access to individuals with theoretical and practical knowledge
in microbiology to provide assistance in areas in which the persons responsible for the program may not have adequate knowledge
and understanding. It should be noted that microbiology is a scientifically based discipline that deals with biological principles
substantially different from those of analytical chemistry and engineering disciplines. Many times it is difficult for individuals without
specific microbiological training to make the transition.

LABORATORY RESOURCES
The laboratory management is responsible for ensuring that the laboratory has sufficient resources to meet the existing testing
requirements. This requires some proficiency in budget management and in determining appropriate measures of laboratory
performance. A measure of laboratory performance is the number of investigations performed on tests conducted by the laboratory,
but this measure alone is not sufficient. In addition to tracking investigations, the period of time between sample submission and
initiation of testing should be tracked, as well as the period of time between end of test and report release (or test closure).
Significant delays in these measures are also indications of an under-resourced laboratory staff.
The laboratory management should have sufficient budget to meet testing requirements. Particular measures of budgetary
requirements will be specific to the given laboratory, but budgetary considerations related directly to the need of the laboratory for
sufficient resources must be addressed to ensure reliable testing results.

DOCUMENTATION
Documentation should be sufficient to demonstrate that the testing was performed in a laboratory and by methods that were
under control. This includes, but is not limited to, documentation of the following:
• Microbiologist training and verification of proficiency
• Equipment validation, calibration, and maintenance
•
•
•
•
•
•
•

• Date
• Material tested
• Microbiologist's name
• Procedure number
• Document test results
• Deviations (if any)
•
•

records. Equipment temperatures (water baths, incubators, autoclaves) should be recorded and traceable.
The governing SOP and revision should be clearly noted in the write-up. Changes in the data should be crossed off with a single
line and initialed. Original data should not be erased or covered over.
Test results should include the original plate counts, allowing a reviewer to recreate the calculations used to derive the final test
results. Methods for data analysis should be detailed in cited SOPs. If charts or graphs are incorporated into laboratory notebooks,
they should be secured with clear tape and should not be obstructing any data on the page. The chart or graph should be signed by
the person adding the document, with the signature overlapping the chart and the notebook page. Lab notebooks should include
page numbers, a table of contents for reference, and an intact timeline of use.
All laboratory records should be archived and protected against catastrophic loss. A formal record retention and retrieval program
should be in place.

INTERPRETATION OF ASSAY RESULTS

Analytical microbiological assay results can be difficult to interpret for several important reasons: (1) Microorganisms are
ubiquitous in nature, and common environmental contaminants—particularly organisms associated with humans—predominate in
many types of microbiological analysis; (2) the analyst has the potential to introduce contaminating organisms during sample
handling or processing in the laboratory; (3) microorganisms may not be homogeneously distributed within a sample or an

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environment; and (4) microbiological assays are subject to considerable variability of outcome. Therefore, apparent differences from
an expected outcome may not be significant.
Because of these characteristics of microbiological analysis, laboratory studies should be conducted with the utmost care to avoid
exogenous contamination as previously discussed in this chapter. Equally important, results must be interpreted from a broad
microbiological perspective, considering not only the nature of the putative contaminant, but the likelihood of that organism(s)
surviving in the pharmaceutical ingredient, excipient, or environment under test. In addition, the growth characteristics of the
microorganism should be considered (especially in questions of the growth of filamentous fungi in liquid media).
When results are observed that do not conform to a compendial monograph or other established acceptance criteria, an
investigation into the microbial data deviation (MDD) is required. There are generally two distinct reasons for the observation of
microbial contamination that does not comply with a target or requirement: There may be either a laboratory error or laboratory
environmental conditions that produced an invalid result, or the product contains a level of contamination or specific types of
contaminants outside established levels or limits. In either case, laboratory management and, in most cases, the Quality Unit should
be notified immediately.
A full and comprehensive evaluation of the laboratory situation surrounding the result should be undertaken. All microbiological
conditions or factors that could bring about the observed condition should be fully considered, including the magnitude of the
excursion compared to established limits or levels. In addition, an estimate of the variability of the assay may be required in order to
determine whether the finding is significant.
The laboratory environment, the protective conditions in place for sampling, historical findings concerning the material under test,
and the nature of the material, particularly with regard to microbial survival or proliferation in contact with the material, should be
considered in the investigation. In addition, interviews with the laboratory analyst(s) may provide information regarding the actual
conduct of the assay that can be valuable in determining the reliability of the result and in determining an appropriate course of
action. If laboratory operations are identified as the cause of the nonconforming test outcome, then a corrective action plan should
be developed to address the problem(s). Following the approval and implementation of the corrective action plan, the situation
should be carefully monitored and the adequacy of the corrective action determined.

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