Microbiology

Introduction

The objective of this user manual is to provide basic information to the users of the Microbiology Unit services on appropriate selection, collection and proper management of microbiological specimens so as to obtain clinically relevant laboratory results in the diagnoses of infectious diseases.

Note: Only Blood Culture & Sensitivity and Urine Culture & Sensitivity tests are MS ISO 15189 accredited.

Fatimah Azlina Binti Ahmad
Normadehah Binti Mohd Rozali
Mohd Shah Ridzal Abdul Rahman
Mohan Rao A/L Chuda Mani

Completing Microbiology Request Form

Request for a specific test can be done by using Microbiology request form or/and Care2x System. Microbiology request form contains two copies, where each copy is different at the back page. Each specimen should be accompanied by fully completed Microbiology request form including the following information:

a. Patient’s Name, Age and Sex
b. Patient’s registration number (PID)
c. Name of Ward or Clinic
d. Relevant clinical history and provisional diagnosis
e. Doctor’s name (stamped) and signature
f. Type of specimen
g. Date and time of specimen collection
h. Test requested (to state clearly the specific test required)
i. Antibiotics/procedure, if any, that the patient is receiving

*This information is important to accurately interpret results and relate the results to patient care

Specimen Labeling

Each specimen shall have a label firmly attached to the specimen container and bearing the following information:

Patient’s name
Patient’s registration number (PID)
Name of Ward or Clinic
Type of specimen (including specific anatomic site)
Date and time of specimen collection

STAT Specimen (Urgent Priority Specimen)

STAT specimen is defined as specimen from patient with potentially life threatening illnesses requiring immediate attention.
All STAT specimens must inform the lab immediately before sending sample. Any other specimen request for urgent processing that not listed below need prior consultation with a Clinical Microbiologist.
STAT specimens are processed immediately upon arrival at the laboratory. STAT specimens include:
1. Blood for culture
2. Cerebrospinal fluid (CSF) – from lumbar puncture procedure or direct sampling in operating theatre
3. Eye specimens – in cases of endophthalmitis
4. Joint fluids – if septic arthritis is diagnosed
5. Pericardial fluid
6. Serum specimen from victim of needle-prick injury for anti-HBs
7. Serum specimen from source of needle-prick injury for anti-HIV
8. Serum specimen from source of needle-prick injury for HbsAg
9. Serum specimen from source of needle-prick injury for Anti-HCV

List of Available Test, Sample Collection, Transportation

Bacteriology Tests

Test	Type of Specimen	Specimen Collection	TAT
Culture & Sensitivity	Blood	Bactec® Plus + Aerobic/F: 8 - 10 ml (Adult) Bactec® Plus + Anaerobic/F: 8 - 10 ml (Adult) Bactec® Peds Plus/F: 1 - 3 ml (Paed / Neonates)	Negative culture result: 6 days from the date sample is received Positive culture result: 3 - 8 days from the date sample is received (depends on time of growth detection by the Bactec® system)
Fungal Culture (on request)	Blood	Bactec® Myco/F-Lytic: 1 - 5 ml	Negative culture result: 4 weeks from the date sample is received Positive culture result: 4 - 6 weeks from the date sample is received (depends on time of growth detection by the Bactec® system)
Culture & Sensitivity	Urine	10 ml urine in a sterile container	2 - 5 days from the date sample is received
Culture & Sensitivity	Sputum	Early morning sputum in sterile container	3 - 6 days from the date sample is received
Ova and cyst (wet mount)	Stool	Fresh stool in sterile container	1 day from the date sample is received
Culture & Sensitivity	Stool	Sterile container	6 days from the date sample is received
Culture & Sensitivity	Cerebrospinal fluid (CSF)	0.5 to 3 ml in a sterile container	3 - 6 days from the date sample is received
Culture & Sensitivity	Pus (wound) swabs	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Aspirates from abscesses or deep wound	Sterile container	3 - 6 days from the date sample is received
Culture & Sensitivity	Tissue & Biopsy	Sterile container	3 - 6 days from the date sample is received
Culture & Sensitivity	Conjunctival (eye) Swab	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Throat swab	Swab in transport media	3 days from the date sample is received
Culture & Sensitivity	Ear Swab	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Intravenous catheter tips	Sterile container	3 days from the date sample is received
Culture & Sensitivity	High vaginal swab	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Endocervical swab	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Urethral swab (male)	Swab in transport media	2 - 5 days from the date sample is received
Body Fluid Analysis	Cell count	Sterile container	2 hours from the time sample is received
Culture & Sensitivity	Sterile body fluids (pleural, pericardial, synovial, intraocular fluid, peritoneal)	Sterile container	2 - 5 days from the date sample is received
Culture & Sensitivity	Nasal swab for MRSA Screening	Swab in transport media	2 - 5 days from the date sample is received
Culture & Sensitivity	Endotracheal Tube (ETT) secretions (tracheal aspirate)	Sterile container	2 - 5 days from the date sample is received
Culture & Sensitivity	Bronchiol Alveolar Larvage (BAL) / Bronchial Washing / Bronchial Brushing	Sterile container	2 - 5 days from the date sample is received

Mycobacteriology Test

Test	Type of Specimen	Specimen Collection	TAT
AFB Detection	Sputum	5 - 10 ml early morning sputum collected in sterile container	1 days from the date sample is received
AFB Detection	Sterile body fluid (other than CSF)	5 - 10 ml in sterile container	1 days from the date sample is received

Serology Test

Test	Type of Specimen	Specimen Collection	TAT
Hepatitis B surface antigen (HBsAg)	Blood / Serum	3 ml in plain tube	3 days from the date sample is received
Hepatitis B surface antibody (anti-HBs)	Blood / Serum	3 ml in plain tube	3 days from the date sample is received
Human immunodeficiency virus antigen/ antibody (HIV Ag/Ab)	Blood / Serum	3 ml in plain tube	3 days from the date sample is received
Hepatitis C virus antibody (anti-HCV)	Blood / Serum	3 ml in plain tube	3 days from the date sample is received
RPR anti-nontreponemal screening for syphilis	Blood / Serum	3 ml in plain tube	1 day from the date sample is received
Dengue NS1/IgM/IgG	Blood / Serum	3 ml in plain tube	2 hours from the time sample is received
Leptospira IgM/IgG	Blood / Serum	3 ml in plain tube	2 days from the date sample is received
Rotavirus	Stool	Sterile container	1 day from the date sample is received
Blood film for malarial parasites (BFMP)	Blood	2 ml in EDTA tube	6 hours from the time sample is received
Needle Prick Injury Screening (Urgent)	Blood	3 ml in plain tube	1 day from the date sample is received

Outsource Tests

Test	Type of Specimen	Specimen Collection	TAT
Human immunodeficiency virus antigen / antibody (HIV Ag/Ab) Confirmation	Blood / Serum	3 ml in plain tube	6 weeks from the date sample is received
Hepatitis B surface antigen (HBsAg) Confirmation	Blood / Serum	3 ml in plain tube	6 weeks from the date sample is received
Hepatitis C virus antibody (anti-HCV) Confirmation	Blood / Serum	3 ml in plain tube	6 weeks from the date sample is received
Mycoplasma Serology	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Toxoplasma IgM/IgG	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Cytomegalovirus IgM/IgG (IgM/IgG CMV)	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Herpes Simplex Virus Types 1&2 IgG	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Epstein-Barr virus (EBV)	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Torches Serology	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Adenovirus Test	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Enterovirus Test	Blood / Serum	3 ml in plain tube	1 month from the date sample is received
Swab specimens for viral culture (Respiratory Syncytial Virus (RSV)	Swab	Viral Transport Medium (VTM)	1 month from the date sample is received
Treponema pallidum particle agglutination (TPPA)	Blood / Serum	3 ml in plain tube	3 days from the date sample is received
Other outsource test	-Please contact Microbiology Unit-	-Please contact Microbiology Unit-	1 month from the date sample is received

Guidelines for Management of Specimen

General Guidelines for Proper Specimen Collection
1. Specimens should be collected before antibiotics given, if possible. If antibiotics are given, indicates in the request form.
2. Specimens should be collected from correct anatomic sites using proper sterile techniques to avoid contamination from indigenous flora.
3. Specimens collected should be adequate of volume and be placed in appropriate container. Inadequate amounts of specimen may yield to false-negative results.
4. Identify the specimen source and/or specific site correctly so that proper culture media will be selected during processing in the laboratory.
5. Check expiration date of the container or transport media before taking specimen. Transport medium prevents specimen drying, helps maintain pathogen viability between collection and inoculation and retards the growth of microbial contamination.
General Guidelines for Proper Specimen Transportation
1. Each specimen should be accompanied by fully completed request via care2x systems. Form will only be used when there is a problem with the internet network only.
2. Properly collected specimens should be sent to laboratory promptly within office hours without delay (preferably within 2 hours). This is to ensure the survival and isolation of pathogens and to provide a more accurate diagnosis of the infectious- disease process.
3. Specimens for viral culture should be delivered on wet ice or a cold pack.
4. If delayed transportation is anticipated, store the specimen at appropriate temperature to maintain its viability.
Guidelines for Bacteriology Tests
1. Blood Culture & Sensitivity
  1. Choose the appropriate culture media to be inoculated and know the optimal blood volume for inoculation.
  2. Check blood bottle medium for gross contamination before use. Bottle with gross turbidity should be returned to the laboratory.
  3. The operator should wear sterile gloves after proper hand washing.
  4. Disinfection the skin area of venepuncture site:
    - Clean the site with 70% alcohol or 2% chlorhexidine or iodine based preparation. If povidone iodine is used, wait for 2 minutes to dry, or if tincture of iodine is used, wait for 30 seconds.
    - Swab the disinfectants on the skin beginning in the centre of the area and moving outward in concentric circles.
2. Do not palpate vein at this point.
3. Remove the outer seal and cap from each blood culture bottle.
4. Disinfect culture bottle with apply 70% alcohol to rubber stopper and wait 1 minute.
5. Inoculate the blood specimen into the blood culture medium by inserting the needle through the rubber stopper.
6. Inoculate a second blood culture bottle without changing the needle. Changing the needle before inoculating the second bottle creates a risk of contamination. Mix the contents of the culture bottle by gentle swirling.
7. Factors directly influencing blood culture results:
  1. Volume of blood collected
  2. Method of skin disinfection
8. General recommendation for blood Culture & Sensitivity collection are as follow:
  1. Acute sepsis: 2 - 3 sets from separate sites all within 10 minute
  2. Acute endocarditis: 3 sets from 3 sites over 1 - 2 hours
  3. Subacute endocarditis: 3 sets from 3 sites taken > 15 minutes apart
  4. Fever of unknown origin: 2 - 3 sets from separate sites > 1 hour apart
9. Only one blood culture bottle should be inoculated at one time from one venepuncture site.
10. Send specimen to lab immediately. If delay is inevitable keep bottle culture at room temperature for not more than 24 hours.
Urine Culture & Sensitivity
1. Date and time of collection of urine specimens are very critical information and must be stated clearly in the request form and specimen container. If this information is not provided, the urine specimen may be rejected.
2. The specimen should reach the laboratory within 1 hour after collection. In case of delay, store urine at 4°C (refrigerated) for not more than 24 hours.
3. The request form should indicate patient is symptomatic or not and method of urine collection. This information is critical to quantitative culture interpretation, especially of low-count urine specimens.

METHOD OF URINE	SELECTION, COLLECTION AND TRANSPORTATION
Catheters Urine	For indwelling urinary catheter, urine must be taken only from the sampling port of the catheter after meticulous preparation of the port. Never collect urine from the bag. Urinary catheter tips are not acceptable specimens for culture. Urine obtained by a straight catheter from women is usually acceptable for culture if attention to site preparation has been accomplished and aseptic collection is successful. Catheter should clean with an alcohol pad. Use a sterile needle and syringe to puncture and aspirate the urine from the proximal lumen or sampling port of the catheter. Transfer the urine into a sterile specimen container.
Midstream (Clean-Catch) Urine	The specimen should be collected after the patient has been given specific instructions. Do not assume that a patient knows how to do what is expected. Collect 2 – 10 ml midstream urine in a sterile container. Early morning urine is preferable to enable the organism to multiply in the bladder before collection. If not possible a period of 2 hours must elapse after the last urination. For Male patient, cleanse the glans (the head of the penis) with plain soap and water. For Female patient, should similarly cleanse the genital area. Discard the first portion of voided urine and collect the midstream urine directly into a sterile bottle.
Suprapubic Aspirate urine	The method is particularly useful in paediatric patients, patients with a spinal cord injury, and patients for whom a definitive culture has not been obtained. This method is required for diagnosing anaerobic urinary tract infections. Decontaminate the skin (with antiseptics as in preparation for surgery) from the umbilicus to the urethra. Anaesthetize the skin at the insertion site. Introduce the needle into the full bladder at the midline between the symphysis pubis and the umbilicus, 1-2 cm above the symphysis pubis. Aspirate about 20 ml of urine from the bladder. Transfer the urine aseptically into a sterile screw-capped container.
Bladder Washout	The method is particularly useful in paediatric patients, patients with a spinal cord injury, and patients for whom a definitive culture has not been obtained. This method is required for diagnosing anaerobic urinary tract infections. Decontaminate the skin (with antiseptics as in preparation for surgery) from the umbilicus to the urethra. Anaesthetize the skin at the insertion site. Introduce the needle into the full bladder at the midline between the symphysis pubis and the umbilicus, 1-2 cm above the symphysis pubis. Aspirate about 20 ml of urine from the bladder. Transfer the urine aseptically into a sterile screw-capped container.
Nephrostomy Tube Urine	To collect this type of urine: Clean the catheter with an alcohol pad. Use a sterile needle and syringe to puncture and aspirate the urine from the catheter. Transfer the urine into a sterile specimen container.

Sputum Culture & Sensitivity
Sputum may not be the best specimen for determining the etiologic agent of bacterial pneumonia (Broncho-alveolar lavage or blood specimens may be more accurate).
Sputum specimens are rejected if microscopic examination reveals epithelial cells, which indicated contamination from the oropharyngeal flora. In such cases, the specimen should be recollected. Careful attention to the instructions given the patient greatly reduces the number of inappropriate specimens.
Send specimen immediately to laboratory. If delay unavoidable store it in refrigerator for not more than 24 hours.
Pooled specimens are not recommended for culture.

METHOD OF SPUTUM	SELECTION, COLLECTION AND TRANSPORTATION
Sputum (Expectorate)	To collect this type of sputum: Have patient rinse and gargle water to remove superficial flora Instruct patient to cough deeply to produce lower respiratory specimen and collect early morning sputum in a sterile container. Instruct the patient in the difference between sputum and spit.
Sputum (Induced)	To collect this type of sputum: Have the patient rinse the mouth with water after brushing the gums and tongue. With the aid of nebulizer, have the patient inhale ~25 ml of 3 - 10% sterile saline. Collect the induced sputum in a sterile container.

Stool Culture & Sensitivity / Rotavirus
1. Instruct patients to excrete directly into the cup or collection device.
2. Alternatively, using a swab collect about one third of the container by dipping and rotating in the faeces taking care to include materials containing pus, mucus or blood if present.
3. Places the stool into a sterile container, screw the cap tightly and send it immediately to the laboratory.
4. Do not allow urine to contaminate the specimen and never take a specimen from the water in a toilet.
5. Routine cultures are done for isolation of Salmonella spp., Shigella spp., Campylobacter spp., Aeromonas hydrophila, EHEC, EPEC. If other agents are suspected, request specifically to the laboratory.
6. Stool specimens for bacterial culture and sensitivity testing must be transported to the laboratory within 1 - 2 hours after collection for immediate processing. Stool specimens that are received more than 24 hours after collection would be rejected. If delay is unavoidable, store at 4°C not more than 24 hours in respective ward.
Cerebrospinal Fluid (CSF) Culture & Sensitivity
1. Disinfect the skin over the lumber puncture site.
2. Using strictly aseptic techniques perform a lumbar puncture and collect about 0.5 - 3 ml of CSF directly into sterile container.
3. Send the specimen immediately to the laboratory.
4. Do not store in a refrigerator as organisms causing meningitis are usually very sensitive to cold.
Wound Swabs Culture & Sensitivity
1. When the lesion is larger or when there are several lesions, multiple specimens from different sites must be collected.
2. Surface lesion samples are unsuitable for anaerobic studies.
3. For collection & transportation:
  - Remove as much of the superficial flora as possible by decontaminating the lesion using sterile swab.
  - Place the swab in appropriate transport medium.
  - Label the specimen and state the names of the specific anatomic
  - locations that are the sources of specimens.
  - Send the specimen immediately to the laboratory.
Aspirates from Abscesses or Deep Wound Culture & Sensitivity
1. Disinfect the surface with 70% alcohol and then with povidone-iodine solution.
2. Aspirate abscess fluid from the deepest portion of the lesion with a sterile syringe and needle and transfer into sterile container (Avoid contamination by the wound surface).
3. Do not allow air to enter the transport container, some anaerobic organisms are killed by oxygen.
4. Send the specimen immediately to the laboratory. Do not store in a refrigerator.
Tissue & Biopsy Culture & Sensitivity
1. Collect tissue aseptically and transfer into a sterile container.
2. Do not place the tissue or biopsy in a fixative solution (formalin). If necessary, moistened the tissue with 0.85% normal saline to prevent drying.
3. Send immediately to the laboratory.
Eye Swab Culture & Sensitivity
1. Specify and state the specific sources of specimens (e.g., conjunctival eye, aqueous or vitreous sample, etc.) and eye side (e.g., left or right eye).
2. In bilateral conjunctivitis, culture of a specimen from only one eye is necessary.
3. For conjunctival swab, purulent material should collect on a sterile cotton swab from the lower conjunctiva sac without contamination with eyelid. The swab should be placed in Amies transport media and transport immediately to the
4. laboratory.
5. Specimen should be collected before application of antibiotics, irrigating solution or other medicines
Throat Swab Culture & Sensitivity
1. The sample is taken at the back of throat and tonsillar areas of inflammation and exudates. Success with culture depends on firmly and completely sampling the involved areas.
2. Insert the sterile cotton swab carefully but firmly into mouth and rub the swab over several areas of exudates or over the tonsils and posterior pharynx.'
3. Do not touch the cheeks, teeth, or gums with the swab so as to avoid.
4. Place the swab in Amies transport medium and send to the laboratory immediately.
Ear Swab Culture & Sensitivity
1. The external ear canal is cleaned with a sterile swab moistened with sterile saline.
2. Pass a swab gently into the external canal and collect the pus or exudates from the middle or inner ear by using a sterile swab.
3. Place the specimen in appropriate transport medium and send to the laboratory immediately.
4. Label the specimen and state in request form the names of the specific anatomic locations that are the sources of specimens.
Intravenous Catheter Tip Culture & Sensitivity
1. Relevant clinical history that should accompany specimen includes:
  - Any suspected or proven infection
  - Duration of cannulation
  - Anatomical location and designated purpose for the cannulation
  - Any antimicrobial therapy received by patient while the catheter was in place
  - Any sign of inflammation at the catheter site (e.g., presence of purulent and lymphangitis, erythema, tenderness, increased warmth, palpable thrombosed vein
2. It is important that the skin surface is cleaned up from any antimicrobial ointment or blood clot before removal of the catheter.
3. Aseptically cut 1 to 4 inches of the distal tip of the catheter using a pair of sterile scissors. Allow the cut segment to drop directly into a sterile container.
4. Send the specimen immediately to the laboratory to avoid drying of the catheter tip.

High Vaginal Swab (HVS) Culture & Sensitivity
1. Use a speculum without lubricant.
2. Obtain secretion from the mucosa high in the vaginal canal with a sterile swab.
3. Place the specimen in appropriate transport medium and send to the laboratory immediately.
Endocervical Swab Culture & Sensitivity
1. Routine tests are done for detection of Neisseria gonorrhoea, Candida spp. and Trichomonas vaginalis.
2. Moisten the speculum with sterile saline. Do not use lubricants as it can be toxic to Neisseriae.
3. Remove from the cervical of any mucous or vaginal material before collecting endocervical discharge with a swab. Alternatively, insert the swab into the cervical os, allow it to remain in place for a few seconds, and remove it.
4. Add a small quantity of sterile saline to the swab specimen to keep it moist before sending it promptly to the laboratory. Do not refrigerate the specimen.
Urethral Swab (Male) Culture & Sensitivity
1. This specimen is useful for definitive diagnosis of gonorrhoea in male patients.
2. Remove the external skin flora of the urethral meatus as in preparation for obtaining a urine specimen.
3. Collect the express exudates from the urethra and collect by using the sterile swab and place the swab in appropriate transport medium. Material from a site about 2 cm inside the urethra or expressed pus is the specimen of choice.
4. If exudates is unavailable, insert a urethrogenital swab about 2 - 4 cm into the urethral lumen, gently rotates it. Leave the swab in place for at least 2 seconds to facilitate absorption before removing it.
5. Send the specimen to the laboratory immediately. Do not refrigerate specimen.
Sterile Body Fluids (Pleural, Pericardial, Synovial, Intraocular Fluid, Peritoneal) Culture & Sensitivity
1. These body fluids are diagnostic for infection if cultures become positive because they are sterile.
2. For peritoneal fluid specimen, a volume of 30 - 50 ml is needed.
3. Clean the needle puncture site with 70% alcohol or 2% chlorhexidine followed by 1% iodine in 70% alcohol or povidone iodine.
4. Aseptically perform percutaneous aspiration to obtain pleural, pericardial, peritoneal, or synovial fluids.
5. Transfer fluids aspirated aseptically to a sterile container and send to the lab without delay.
Nasal Swab for MRSA Screening
1. Lesions in the nose require samples from the advancing margin of the lesion.
2. Nasal swab culture is routinely done only for MRSA screening.
3. Carefully insert sterile swab at least 1 cm into the nostril and firmly sample the membrane by rotating the swab and leaving it in place for 10 to 15 seconds. Then, withdraw the swab and insert it in a transport container.
4. Use separate swabs for each nostril.
5. Detection of carriage of methicillin-resistant S. aureus (MRSA) can be increased by also sampling another body sites, such as the rectum and axilla.
Endotracheal Tube (ETT) Secretions (Tracheal Aspirate) Culture & Sensitivity
1. Collect the specimen through atracheostomy or endotracheal tube(ETT).
2. Carefully pass the catheter through the site and into the trachea.
3. Aspirate material from the trachea using a syringe or an intermittent suction device and place the specimen in sterile container.
4. Send the specimen to the laboratory quickly. Do not refrigerate the specimens.
Bronchiol Alveolar Larvage (BAL) / Bronchial Washing / Bronchial Brushing Culture & Sensitivity
1. Broncho Alveolar Lavage (BAL): 50 to 200 ml of sterile saline is infused into the distal bronchoalveolar tree and subsequently suction out about 10 ml fluid containing cells and microorganisms located at the alveolar level from each
2. specimen trap.
3. Place the fluid in sterile tubes, and submit the specimens to the laboratory.
4. Bronchial Washing: Saline is injected through the bronchoscope and subsequently aspirated from the airways.
5. Bronchial Brushing: A brush is advanced through the bronchoscope and used to abrade suspicious lesions to obtain cells. Bronchial brushings are preferable to washings because the latter specimens are more diluted.
6. Place aspirate or washing in sterile container and send to laboratory immediately. Do not refrigerate the specimen

Guidelines for Mycobacteriology Test:

Sputum for AFB Detection
1. Sputum is preferably collected when the patient first wakes up in the morning.
2. Gargle mouth before sputum collection and ask the patient to spit directly into a sterile container. Ensure that expectorate is sputum and not saliva.
3. Send the specimen immediately to the laboratory. If delay is unavoidable store it in a refrigerator.
Sterile Body Fluid (Other than CSF) For AFB Detection
1. Gastric Content (Gastric Lavage Fluid) - this method is used to examine for M. tuberculosis when sputum specimens are unavailable.
2. Early morning fasting specimen is preferred for mycobacterial culture.
3. The gastric contents of 5 - 10 ml are aspirated and placed in a sterile container.
4. Immediately send the specimen to laboratory.
5. Handle all specimens with the safety precautions necessary for working with M. tuberculosis.

Guidelines for Serology Tests:

Each specimen should accompany by fully completed Microbiology Request Form.
Blood collected in plain container should be allowed to clot by standing undisturbed at room temperature.
Do not refrigerate the specimen (haemolysis increases during refrigeration).
Clear, non-haemolysed specimens are preferred (false positivity is a problem with haemolysed specimens).
Serum is the recommended and best specimen for serological testing.

REQUESTED TEST	VOLUME OF SPECIMEN NEEDED
For single serology test (Adult)	3 ml of blood in one plain tube
For single serology test (Neonates)	Not less than 1.5 ml of blood per bullet.

For Needle Prick Injury Cases (NPI):
1. Please inform lab staff immediately before sending sample.
2. Specimens are send in pairs (except unknown source) and note on the form whether it is victim / staff or patient / source.
3. State the status of NPI case (Review or New case).
4. New case: HBsAg, HCVAb, HIV Ag/Ab and RPR test will be done in 1 working day from the date sample is received.
5. Repeat / Review case: HBsAg, HCVAb, HIV Ag/Ab and RPR test will be done within 7 days from the date sample is received.

Guideline for Outsource Samples

Those tests which are not offered by the Microbiology Unit will be outsourced to Referral Laboratory (Refer APPENDIX: LIST OF REFERRAL LABORATORY).
Prior arrangement must be made with Microbiology Unit staff before submission of specimen.
Each specimen should accompany by fully completed Microbiology (ADL) Request Form.
For combination of many tests (e.g., TORCHES), please send more blood / serum volume in one plain tube (more than 3 ml) instead of many tubes but lesser serum volume.
Swab specimens for viral culture should be transported using appropriate transport medium - Viral Transport Medium (VTM) to prevent drying, and send immediately the specimen to the laboratory on wet ice or a cold pack. Do not freeze or hold the specimen at room temperature.
Microbiology Unit (ADL) staff will send the outsourced specimens to the Referral Laboratories only on Monday and Tuesday morning.

Specimen Rejection

Besides the rejection criteria stated in Chapter 1, 10.1, Microbiology Unit reserves the right to refuse processing any specimen that has any of the following characteristics
1. Inappropriate temperature of the specimen during transportation.
2. Prolonged transportation time / transport media already dried up.
3. Specimen collected in inappropriate transport medium.
4. Presence of contamination detected on gross examination of the specimen.
5. Specimen received in formalin or other fixative for culture.
6. Saliva as a respiratory specimen (instead of sputum).
7. Two or more specimens collected within a 24 hour period (unless requested by the laboratory).
8. Anaerobic specimen not sent under conditions which will preserve anaerobic organism.
9. Unsuitable specimen for culture (for example, swab specimen for anaerobic culture, or Foley catheter tip for culture).
10. Culture for Gonococci is not suitable for specimen HVS (only accept for endocervical swabs, cervical swab and vaginal discharge).
The clinic / ward / test requester will be notified before a statement of specimen rejection is issued by the laboratory. Processing of compromised specimen is the onus of the test requester and microbiology consultation should be sought.
Any compromised specimen that cannot be easily re-collected, or that has been harvested as part of an invasive procedure (i.e. aspirates, sterile body fluids and tissues) will be processed only upon obtaining documented agreement from the test requester. The laboratory reports will contain the specification of the specimen’s compromised qualities to indicate that the result generated may not be accurate and test results should be interpreted with caution

Release of Results

Preliminary report
1. Preliminary report is available when result is crucial to patient management.
2. For Blood C&S test:
  1. Routine blood culture bottle (Aerobic, Anaerobic, Paeds) are incubated in BACTEC machine for up to 5 days incubation and 28 days for SBE/IE, Brucella/Cat Scratch Disease, 30 days for blood fungal, while 42 days for blood Mycobacterium.
  2. If positive blood culture bottle is flagged by machine, Gram Stain of the blood culture is performed and will be verbally informed immediately to the ward / clinic / test requester. Then, Primary Antibiotic Susceptibility Test (AST) will be informed verbally on the next day (if applicable). All telephoned communications is recorded and printed reports will be followed.
For CSF C&S test:
1. 1. All CSF microscopic result will be informed via phone immediately to the ward / clinic / test requester. All telephone communications is recorded.
  2. If CSF culture is growth (positive), result will be informed via phone immediately to the ward / clinic / test requester and a printed report will followed.

Critical Notification Values

TYPE OF SPECIMEN / TEST	ORGANISM
Blood & CSF C&S	All Positive final result
All type of specimens for C&S	Methicillin Resistant Staphylococcus aureus (MRSA)  Extended Spectrum Beta Lactamases (ESBL) Carbapenem Resistant Enterobacteriaceae (CRE) Multidrug Resistant Organisms (MRO) – include Acinetobacter Vancomycin Resistant Enterococci (VRE) Salmonella spp./ typhi Shigella spp Streptococcus pneumoniae Streptococcus Group A Haemophilus influenzae Neisseria gonorrhoeae Vibrio cholerae Aeromonas hydrophila Burkholderia mallei/ pseudomallei Clostridium perfringenes Corynebacterium diphtheriae Enterohemorrhagic Escherichia coli EHEC) Mycobacterium tuberculosis
Serology Test	All Positive testing results

Notification Result

When a result warrants a notification of a communication disease under the Notification Communicable Disease of Malaysia via Prevention and Control of Infectious Disease Act 1998, results that is ready to dispatch will be informed via phone immediately to Unit Kawalan Jangkitan (UKJ) IPPT and respective ward / clinic / test requester, whether it is new or review case.

References

Advanced Diagnostic Laboratory (ADL) Advanced Medical And Dental Institute, Universiti Sains Malaysia (2018) Quality Procedure On Sample Management (AMDI/ADL/QP-15)
Clinical and Laboratory Standard Institute (CLSI). Principles and Procedures for Blood Cultures; Approved Guideline. CLSI document M47-A (ISBN 1-56238-641-7). Clinical and laboratory Standards Institute, 950 West Valley Road, Suite 2500, Wayne Pennsylvania 19087 USA, 2007.
Communicable Disease Surveillance Section, Disease Control Division, Ministry of Health Malaysia (2004) Syndromic Notification And Laboratory Investigation Manual (2nd Edition). MOH / K / EPI / 38.04 (HB)
Department of Medical Microbiology & Parasitology School of Medical Sciences Health Campus (2019) Guidelines For Selection, Collection And Management Of Microbiological Specimens (Seventh Edition). MMPP/DD/10.
Health Education Division, Ministry of Health Malaysia (2017) Alert Organisms. (http://www.myhealth.gov.my/en/94404/)
Institute for Medical Research (IMR) Ministry of Health Malaysia (2012) Standard Operating Procedure for Transport of Biological Specimens in Malaysia (1st Edition).
Miller J. M., Miller S. A. (2017) A Guide to Specimen Management in Clinical  Microbiology, Third Edition. American Society for Microbiology, Washington, DC.
Miller J. M., Binnicker M. J.,Campbell S., Carroll K. C., Chapin K. C., Gilligan P. H., Gonzalez M. D., Jerris R. C., Kehl S. C., Patel R., Pritt B. S., Richter S. S., Robinson- Dunn B., Schwartzman J. D., Snyder J. W., Telford III S., Theel E. S.,Thomson Jr R. B., Weinstein M. P., and Yao J. D. (2018) A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology.  https://academic.oup.com/cid/article-abstract/67/6/e1/5046039
Pathology Department of Hospital Pulau Pinang (2016) User Manual of Pathology and  Transfusion Medicine Services (Fifth Edition)
Saskatchewan Health Authority (2016) Critical And Semi-Urgent Notification Values For  Clinical Microbiology. https://www.saskatoonhealthregion.ca/locations_services/ Services/PathologyLaboratoryMed/healthpractitioners/Pages/criticalandsemiurgentvalue sforclinical microbiology.aspx

Referral Laboratory

Department of Medical Microbiology & Parasitology School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan. Tel: 09-7676286 Fax: 09-7676289
Pathology Department Ground Floor, Block B, Hospital Pulau Pinang. Tel: 04-2225145 Fax: 04-2225155 
Institute for Medical Research (IMR) Jalan Pahang, 50588 Kuala Lumpur. Tel: 03-2698 6033 Fax: 03-56939335 
Makmal Kesihatan Awam Kebangsaan (MKAK) Lot 1853, Kg Melayu Sungai Buloh, 47000 Sungai Buloh, Selangor. Tel: 03-6156 5109 Fax: 03-6140 2249
Innoquest Pathology Sdn. Bhd.
Lablink Medical Laboratory Sdn. Bhd.

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