MED-002-Microbiology-29-Mar-2019
MED-002-Microbiology-29-Mar-2019
MED-002-Microbiology-29-Mar-2019
Personnel
Accommodation & Environmental Conditions
- Physical Facilities and Laboratory Safety
Laboratory Equipment – Calibration & Maintenance
Pre-examination Procedures
– Requisitions, Collection and Handling of Specimens
Examination Procedures
- Test Methods and Method Validation
Assuring Quality of Examination Procedures
- Quality Control, Proficiency Testing, Reagents and Reference
Materials
Post-examination Procedures
- Retained Samples and Waste Disposal
Reporting of Results
3. Personnel
3.1 Refer to Personnel in General Technical Note: Medical - 001.
4.2.3 Autoclave: All persons using the autoclave should have been trained and
demonstrate competence in its operation. Face shields and protective
aprons should be used for unloading liquids. Heat-proof gloves should
be available for unloading the autoclave.
4.3 Mycobacteriology
4.3.1 The laboratory shall be assessed according to the types of tests offered:
Acid-fast smear, Molecular diagnosis and Mycobacterial culture and
identification. A risk assessment should be done and safe work practices,
accommodation and environment provided to minimize risk of
transmission to staff. The use of a BSL-3 or equivalent facility for TB
culture work will need to be in compliance with requirements under the
Biological Agents and Toxins Act.
5. Equipment:
5.3 Parasitology
5.3.1 A calibrated ocular micrometer is required for the measurement of eggs
cysts and larva.
6. Pre-examination Procedures
6.1 Refer to Pre-examination Procedures – Requisitions, Collection and
Handling of Specimens in General Technical Note: Medical - 001.
7. Examination Procedures
7.1 Bacteriology
7.1.2 Urine cultures: The laboratory should perform and report quantitative
cultures and use media and procedures that permit isolation of clinically-
relevant Gram positive and negative bacteria. Specimens should be
processed in a timely manner so that bacterial overgrowth does not occur
in the urine. Where delay in plating is expected, provision should be
made to prevent overgrowth: viz. storing at 4 deg C, or by adding
preservative to the container, and or using dip slide cultures. For dip
slide cultures, there must be evidence that the estimated counts correlate
with actual colony counts.
7.1.3 Urethral and Cervical cultures: Transport and culture conditions should
be satisfactory for the isolation of N.gonorrhoeae.
7.1.6 Blood cultures: Sterile technique for drawing and handling blood cultures
should be defined. The blood culture system shall be designed to recover
both aerobic and anaerobic organisms. Sub-cultures and/or stains need
not be done on blood cultures performed by automated methods if the
bottles are monitored as recommended by the vendors. There shall be a
policy for immediate notification of positive blood results
7.1.7 Wound cultures: When indicated, Gram stain of direct smears should be
examined and reported. Both aerobic and anaerobic cultures should be
performed on specimens from appropriate sites.
7.2 Mycobacteriology
7.2.1 Rapid and reliable methods shall be used for microscopic examination,
isolation, identification and antimycobacterial susceptibility testing of
Mycobacterium tuberculosis complex.
7.3 Mycology
7.3.1 Technical procedures for isolation and identification of fungi directly from
specimens and cultures shall be available.
7.4.2 Both thick and thin blood films should be used in the examination for
malarial parasites in suspected cases of malaria.
7.4.3 Stained films should be washed with a buffer of known pH (6.8 - 7.2).
Thick film examination should include at least 100 oil immersion fields
(approximately 10-15 mins).
7.4.4 The physician shall be informed immediately of a blood film positive for
malaria. Where infection by P. knowlesi is suspected, there should be a
process for identification.
8.2 Results of control tests shall be reviewed before reporting patient results.
8.3 There shall be records of at least weekly review of quality control results
by the head or designee.
8.7.1 All reagents, stains, media, kits and antimicrobials should be stored as
recommended by the manufacturers and used within their indicated
expiry dates.
8.7.2 They should be labelled, as applicable and appropriate, with the content
and quantity, concentration or titre date received or prepared, date placed
in service, storage requirements and expiry date. If there are multiple
components of a reagent kit, the laboratory must use components of
reagent kits only with other kits that are of the same lot number unless
otherwise specified by the manufacturer.
8.7.3 New reagent lots shall be checked against old reagent lots or with
suitable reference material before being placed in service.
8.7.4 The use of commercial reagents and controls shall comply with
manufacturer’s instructions.
8.7.5 The laboratory shall have documented records of quality control results of
test procedures, reagents, stains, media, kits, antimicrobials, etc. These
should be checked prior to being placed in service and subsequently be
monitored at specified intervals for performance or limits of acceptability.
Corrective actions should be documented when such results are
unacceptable.
8.7.6 The laboratory shall perform and record results with positive and negative
controls at specified periodic intervals. Recording of qualitative
observations e.g. colour change, should be unambiguous with respect to
the expected result.
8.8 Media
8.8.1 The laboratory shall ensure that all media prepared in-house are sterile,
able to support growth and are appropriately reactive biochemically. This
will require that the laboratory maintains stock reference organisms and
tests the media before or concurrent with use.
8.8.2 For purchased media, the manufacturer shall document to the user that
their quality control activities meet the criteria described as above, 8.9.1
The laboratory should test media that are known to show significant
variability in performance e.g. chocolate agar (for H. influenzae),
campylobacter agar, Thayer-Martin medium
MED 002-Microbiology, 29 March 2019 Page 6 of 10
8.8.3 The user shall visually examine each batch of media for breakage,
contamination, appearance, or evidence of freezing or overheating.
8.8.4 All the quality control procedures that are carried out in the laboratory
shall be documented.
8.8.5 A record should be kept of all lot numbers and expiration dates of the
media received for the past two years.
8.8.6 Reference cultures and sera should be maintained for the proper control
of stains, media, reagents, antimicrobial susceptibility tests and
serological tests.
8.9 Bacteriology
8.9.1 Each new batch of stains (Gram stain, special stains, and fluorescent
stains) should be checked at least weekly with known positive and
negative control organisms for intended reactivity and results recorded.
8.9.2 Guidelines shall be established for the number and type of antibiotics to
be reported for organisms isolated from different sites of infection. They
should be clinically relevant and include suppressing the results of
selected antibiotics to encourage prudent antibiotic use.
8.9.3 Only single isolates or pure cultures shall be used for the final
performance of antibiotic susceptibility testing. Each new lot of antibiotic
discs should be checked for activity before being placed in service and at
least weekly thereafter with reference cultures.
8.9.5 Written criteria shall be available for interpretation of the end point or
zone size.
8.10 Mycology
8.10.1 All stains shall be checked with appropriate positive and negative controls
for each new batch of preparation and at least daily. (For stains like
Gomori’s methenamine silver, the slide itself serves as the negative
control).
8.10.2 Serological (antibody and antigen) and nucleic acid tests should be run
with known positive and negative control organisms or sera with each
new batch of preparation and when appropriate.
8.11.1 Stains
8.11.1.1 Stains for acid-fast bacilli should be checked with known positive and
negative control organisms and the results recorded for each new batch
and thereafter at least weekly or on each day of use (whichever is less
frequent)
8.11.2 Identification
8.11.2.2 Biochemical tests used for identification should be checked each day of
use with appropriate positive controls.
8.12 Parasitology
8.12.2 All permanent stains shall be checked, together with controls, for
intended staining results at least monthly, or with each test if test is
performed less frequently. Special stains used to detect specific
organisms (e.g. acid-fast, fluorescent stains) shall be checked with
appropriate control organisms each time the stain is used.
8.13 Virology
8.13.1 This section applies to any laboratory providing facilities for the diagnosis
of viral infections, which include cell culture, antigen detection, serology
or molecular diagnosis. (Refer to “MOLECULAR PATHOLOGY” section).
8.13.4 Animal sera for use in culture media shall be tested to exclude toxicity to
cells.
8.13.5 Appropriate cell lines should be available to support the services offered
by the laboratory.
8.13.7 Media and diluents shall be checked for sterility and pH.
8.13.8 There shall be documentation of cell types, source, passages and media
used in their propagation.
8.13.9 Worksheets or records shall indicate titres, when known, of reagents and
control sera.
8.13.10 There shall be known positive and negative controls with each run of test
specimens for all direct antigen tests on patient specimens.
9. Post-examination Procedures
There should be suitable facilities for storage of samples that may need
re-testing. There should be a policy on the duration of storage, to allow
retrieval of samples or significant isolates for re-testing or further testing.
Serum shall be stored for an appropriate length of time when paired titres
are expected to be performed.
10.1 Reports with abnormal results shall be reviewed by senior personnel and
evaluated for conformity with the clinical information available