Good Microbiological Laboratory Practice SOP

In short: This illustrative SOP covers staff practices, sample handling, records and biosafety in a pharmaceutical microbiology laboratory. Adapt it to the room, test method, product and risk assessment; use the approved procedures for gowning, equipment, environmental controls and waste.

Objective and scope

Describe routine practices that support reliable microbiological testing and help control contamination and biological hazards in a QC laboratory. This example SOP is scoped to non-sterile pharmaceutical products. This template does not establish cleanroom grades, pressure limits, test conditions or universal personnel restrictions.

WHO Technical Report Series No. 961, Annex 2 (2011), WHO Good Practices for Pharmaceutical Microbiology Laboratories, addresses microbiology personnel, premises, cleaning, environmental monitoring, equipment, media, test methods and reporting. It calls for laboratory arrangements that reflect the work and risk, including controlled access and separation of activities where needed. The same annex has a separate section for sterility-test facilities; apply those additional facility and gowning controls only under the applicable approved sterility-testing procedure. WHO TRS 961, Annex 2 (2011).

Responsibilities

• Microbiology staff and assistants: Follow current approved procedures, use only authorized areas and equipment, record work as it is performed, and report incidents or unexpected conditions.
• Laboratory supervisor or method owner: Maintain the approved procedures, training and area-specific controls for assigned work.
• Quality unit: Review and approve controlled documents according to the site’s quality system.

This example SOP assigns responsibility to a microbiologist or designee and a laboratory assistant, gives the Head of Microbiology implementation responsibility, and assigns SOP approval to QA. Role titles, scope (non-sterile products only; sterility testing needs its own facility procedure) and the approval route must be confirmed in the site’s controlled document system, with the accountable document owner named there.

Procedure

Personnel health, hygiene and clothing

Follow the site’s occupational-health, hygiene and entry procedures. Staff should report symptoms, skin conditions or wounds that could affect safe work or sample integrity to the designated site contact, who should determine the appropriate work restrictions or controls (fitness for work is assessed by the site occupational-health function, not by the laboratory template). Wear clean, suitable laboratory clothing and any hair covering or protective equipment required by the room and activity. Follow the approved procedure for entering, leaving and laundering or replacing garments.

Example in-house criterion (not a pharmacopoeial requirement): This example SOP excludes staff with open wounds, skin conditions or respiratory infection from laboratory work; it also calls for clean covered hair, clean coats or uniforms, trimmed nails, and no jewellery or unnecessary cosmetics. Apply these points through current occupational-health and area-hygiene procedures rather than as unsupported universal rules.

Example in-house criterion (not a pharmacopoeial requirement): The source calls for loose-fitting, non-shedding garments with no external pockets, sealed edges and enclosed seams, cleaning that limits contamination, sterilization before use, and immediate use of an opened sterilized garment. Follow the approved garment and laundering procedure for the actual room classification and test.

Example in-house criterion (not a pharmacopoeial requirement): The source directs personnel not to move unnecessarily, requires maintenance personnel to follow laboratory precautions, and describes using a pass box between unclassified and classified areas. Use the approved access and maintenance-work controls for each room. Keeping articles off a laminar-airflow bench, not leaning into it and opening Petri dishes only inside it are practices to apply only where such equipment is installed, qualified and called for by the test procedure.

Work area, equipment and sample handling

1. Confirm that the area, bench or containment equipment is suitable for the procedure. Use a laminar-airflow bench, biological safety cabinet or other equipment only for the purpose it is qualified and approved to support.
2. Follow the current method for sample preparation, aseptic handling, transfers, mixing and equipment setup. Keep materials arranged to avoid mix-ups and cross-contamination; do not obstruct airflow or place items where the equipment procedure prohibits them.
3. Use glassware, disposable plates and other consumables that meet the method and site procedure. Handle sterile items without compromising their condition.
4. Follow the method and media procedure for storage, equilibration, preparation, labelling, use validity and disposal. Record applicable media, culture and reagent identities and preparation details.
5. Clean and disinfect the work area and equipment under approved procedures. Keep materials and logbooks in their designated locations after work.

The WHO Laboratory Biosafety Manual, fourth edition (2020), recommends a risk- and evidence-based approach to biosafety controls, including work practices, personal protective equipment and decontamination. Use the site’s biological-risk assessment and biosafety procedures to choose controls for the organisms and work performed. WHO Laboratory Biosafety Manual, 4th edition (2020).

Example in-house criterion (not a pharmacopoeial requirement): The source says refrigerated media, cultures and water should reach room temperature before use and that tubes in serial dilutions should be vortexed. The required equilibration and mixing method depend on the material and approved test procedure; do not apply them to every material or every serial dilution without method support.

Environmental conditions and monitoring

Maintain room conditions required by the laboratory design, approved methods and contamination-control plan. Where temperature, humidity, pressure differentials or environmental monitoring are defined as relevant controls, record and review them under the approved monitoring programme. Do not add a room set point, range, frequency or alert/action limit from this template.

Example in-house criterion (not a pharmacopoeial requirement): The source says laboratory humidity and pressure differential should be maintained and recorded but provides no locations, target values, limits or monitoring frequency. Whether these controls apply to a non-sterile laboratory is decided by the approved facility design, risk assessment and monitoring programme; no universal values are given here. WHO TRS 961, Annex 2 (2011), §2.1.4 calls for temperature and humidity controls where required; §2.2.1 describes environmental monitoring where necessary and appropriate, including pressure differentials in relevant areas. WHO TRS 961, Annex 2 (2011).

Records and data integrity

Use the latest effective method and record observations and results as work is performed. Preserve original raw data and their link to the sample, test method, equipment and analyst. Record equipment, media and culture details needed by the method, calculations, deviations and review. Any correction must retain the original information and be signed or attributed and dated; record a reason where appropriate.

For U.S. CGMP operations, 21 CFR 211.194(a) requires complete laboratory test data and records identifying the sample, method, data, calculations, results, performer and second-person review. EudraLex Volume 4, Part I, Chapter 4, Revision 1 (2011), §§4.8–4.9 says records should be completed when actions are taken and that alterations should be signed and dated while keeping the original information readable. Apply each requirement where it governs the operation. 21 CFR 211.194(a), current eCFR; EudraLex Volume 4, Chapter 4.

Example in-house criterion (not a pharmacopoeial requirement): The source requires systematic logbook storage, contemporaneous raw-data entries, and records of humidity and pressure differential. Define required logs and room monitoring in the approved site procedures.

Retain batch-associated GMP records for at least 1 year after the expiry date of the respective product batch. Where EU GMP applies, retain batch documentation for at least 5 years after Qualified Person certification if that period is longer. Follow any longer period required by local law, the marketing authorisation or the approved site schedule. These periods are stated in 21 CFR 211.180(a) (current eCFR) and EudraLex Volume 4, Part I, Chapter 4, Revision 1 (2011), §4.11 (effective 30 June 2011). 21 CFR 211.180(a); EudraLex Volume 4, Chapter 4.

Spill response and waste

Handle cultures and contaminated materials according to the organism-specific risk assessment, approved spill response, decontamination and waste-disposal procedures. Report spills or exposure incidents promptly through the site’s biosafety and EHS channels. Do not dispose of tested plates or media until the approved procedure’s treatment and waste route has been completed.

Example in-house criterion (not a pharmacopoeial requirement): The source directs staff to follow a culture-spill management procedure and decontaminate used media and plates before disposal. The spill response, decontamination method, waste classification and disposal route must follow the organism-specific risk assessment and site biosafety/EHS procedures.

Training

Train personnel on the procedures, equipment, gowning and containment controls relevant to their assigned work. Record initial and continuing training, practical assessment and authorization under the site quality system. For U.S. CGMP operations, 21 CFR 211.25(a) addresses training for assigned functions and continuing training in applicable CGMP. WHO TRS 961, Annex 2 (2011), §1.4 discusses practical training and ongoing competence for microbiological tests; WHO Laboratory Biosafety Manual 4th edition (2020) emphasizes training appropriate to biological-risk controls. Training should match the actual role and work. 21 CFR 211.25(a), current eCFR version up to date as of 14 October 2026.

Frequently asked questions

Does this SOP require sterile garments for every microbiology laboratory?

No. The source’s garment instructions need review against the room and procedure. Sterility-testing facilities and classified areas have their own approved controls; use those procedures when applicable.

Should every microbiology room have a pressure differential and humidity limit?

This template does not set those controls or limits. Apply them where required by the facility design, risk assessment, applicable procedure or product controls.

How should a spill or contaminated plate be handled?

Follow the approved risk-based spill response, decontamination and waste procedure for the material. Record and report incidents as required by site procedures.

See also

• Microbiologist qualification SOP
• Microbiological analytical data review checklist
• Training of employees SOP

References

• World Health Organization, WHO Good Practices for Pharmaceutical Microbiology Laboratories, WHO Technical Report Series No. 961, Annex 2 (2011), especially §§1–2 and 9: official publication.
• World Health Organization, Laboratory Biosafety Manual, 4th edition (2020): official publication.
• United States, 21 CFR 211.25(a), “Personnel qualifications,” current eCFR version up to date as of 14 October 2026: official regulation.
• United States, 21 CFR 211.194(a), “Laboratory records,” current eCFR version up to date as of 14 October 2026: official regulation.
• United States, 21 CFR 211.180(a), “General requirements,” current eCFR version up to date as of 14 October 2026: official regulation.
• European Commission, EudraLex Volume 4, Part I, Chapter 4, “Documentation,” Revision 1 (2011; effective 30 June 2011), §§4.8–4.9 and §4.11: official guidance.