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List Of Test And Sample Collection (Microbiology)

LIST OF AVAILABLE TEST

1. Bacteriology Tests:

  • Cerebro spinal fluid (CSF) Culture & Sensitivity
  • Blood Culture & Sensitivity
  • Urine Culture & Sensitivity
  • Sterile body fluids(pericardial, synovial, intraocular fluid, peritoneal) Culture & Sensitivity
  • Nasal swab Culture & Sensitivity
  • Throat swab Culture & Sensitivity
  • Sputum Culture & Sensitivity
  • Eye (conjunctival) swab Culture & Sensitivity
  • Ear swab Culture & Sensitivity
  • Pus (wound) swab Culture & Sensitivity
  • Aspirates from abscesses or deep wound Culture & Sensitivity
  • Tissue & Biopsy Culture & Sensitivity
  • Stool Culture & Sensitivity
  • Stool FEME for ova and cyst (wet mount)
  • High Vaginal swab Culture & Sensitivity

2. Mycobacteriology Test:

  • Sputum for AFB detection
  • Sterile body fluid (other than CSF) for AFB detection

     3. Serology Test:

  • Anti –streptolysin ‘O’ test (ASOT)
  • VDRL anti-treponemal screening
  • Stool Rotavirus
  • Dengue IgM/IgG
  • HBsAg
  • Anti-HBs
  • Anti HBc
  • Anti HCV
  • HIV
  • Mycoplasma
  • Cytomegalovirus
  • Toxoplasma

SPECIMEN COLLECTION

1. Bacteriology

  • Properly collected specimens should be sent to lab within office hours without delay in order to avoid overgrowth of commensals or loss of viability of pathogens.
  • Specimens should be collected from correct anatomic sites using proper techniques to avoid contamination from indigenous flora.
  • Specimens should be collected before antibiotics given, if possible. If antibiotics are given indicates in the request form.
  • Specimens collected should be of adequate volume and be placed in appropriate container.
  • Each specimen should be accompanied by fully completed request form.
  1. 2 Collection of Cerebrospinal Fluid (CSF) for culture and sensitivity (C & S) or Bacterial Antigen Detection
    1. Disinfect the skin over the lumber puncture site.
    2. Observing 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. DO NOT STORE IN A REFRIGERATOR as organisms causing meningitis are usually very sensitive to cold.
  1. 3 Blood C & S

Check blood medium for gross contamination before use. Bottle with gross turbidity should be returned to the lab.

  1. Disinfection of culture bottle: Apply 70% alcohol to rubber stopper and wait 1 minute.
  2. Disinfection of venipuncture site:
  • Cleanse site with 70% alcohol.
  • Swab concentrically starting at center with iodine and allow iodine to dry.
  • Do not palpate vein at this point.
  • Withdraw 5 – 10ml of blood (adults) or 1 – 2 ml blood for infants.
  • After venipuncture remove iodine from skin with alcohol.
  1. Send specimen to lab immediately. If delay is inevitable keep bottle culture at RT for not more than 24 hours
  2. Bottle culture using Bactec®bottle
  • Adult: 8-10ml -aerobic culture, anaerobic culture, two (2) sets of blood cultures
  • Pead/Neonates: 1-3ml

General recommendation for blood C & S 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 hr.
  3. Subacute endocarditis: 3 sets from 3 sites taken > 15 minutes apart.
  4. Fever of unknown origin: 2 – 3 sets from separate sites > 1 hours apart.

Only one blood culture bottle should be inoculated at one time from one venipuncture site.

  1. 4 Urine for C & S
  1. Collect 2-10ml 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 3 hours must elapse after the last urination.
  2. Male patients, should cleanse the glans penis with plain soap and water after retracting the foreskin.
  3. Female patients should similarly cleanse the labial folds and vulva.
  4. Discard the first portion of voided urine and collect the midstream urine directly into a sterile bottle.

Note: The specimen should reach the laboratory within 1 hour after collection. In case of delay, store at 4◦C for not more than 24 hours.

  1. 5 Catheter tip
    1. Cleanse skin around catheter site with alcohol.
    2. Aseptically remove and clip 5cm distal tip catheter into sterile container and send immediately the lab.
  1. 6 Sterile body fluids for C & S
    1. Transfer pleural, pericardial, peritoneal and synovial fluids aspirated aseptically to a sterile container and send to the lab without delay.
    2. If delay is unavoidable, store at RT for < 24 hours except for pericardial fluid which should be stored at 4◦C.
  1. 7 Nasal Swab for C & S

The swab needs to be moistened with sterile saline before sampling. Rotate the swab over the mucosa of the nasal cavity. Replace the swab in swab transport media and send the specimen to the laboratory immediately.

  1. 8 Throat Swab for C & S
  1. Insert the swab carefully the mouth with the tongue depressed.
  2. Rub swab over each tonsillar area and the posterior pharynx. Any area with exudate should be sampled.
  3. Do not allow swab to touch tongue or lips.
  4. Replace the swab in swab transport media and send to the laboratory immediately.

If Corynebacterium diphteriae is suspected:

  1. Lift edge of the membrane and swab under it.
  2. Obtain at least 2 swabs and send to the lab immediately.
  1. 9 Sputum for C & S

Sputum expectorate

  1. Have patient rinse and gargle water.
  2. Instruct patient to cough deeply to produce lower respiratory specimen and collect early morning sputum in a sterile container.
  3. Send specimen immediately to laboratory. If delay unavoidable store it in refrigerator for not more than 24 hours.
  1. 10 Tracheal aspirate, Bronchiol Alveolar Larvage, bronchial washing
  1. Place aspirate or washing in sterile container or sputum trap.
  2. Send to lab immediately. If delay is unavoidable, store in refrigerator for < 24 hours.
  1. 11 Eye Swab
    1. Collect the exudate with separate sterile swabs.
    2. Place the swab into a transport medium and send it together with a fixed smear of the exudate to the lab.
    3. For the isolation of Neisseria gonorrhoeae, inoculate the specimen onto a Thayer-Martin agar or GC AGAR + LCAT plate in a ‘Z’ fashion by the bedside. Place the plate in an anaerobic jar. Send anaerobic jar as soon as possible to the laboratory.

Note: An anaerobic jar and GC Agar + LCAT is available on request from the laboratory.

  1. 12 Ear Swab
    1. The external meatus is cleaned with a dry swab moistened with sterile saline. Let the site dry before sampling.
    2. Pass a swab gently into the external canal and collect whatever exudate that is found there.
    3. Place the swab in swab transport media and send the specimen to the laboratory as soon as possible.
  1. 13 Collection of Pus Aspirate
    1. Disinfectant the skin over the inflamed area by wiping with sterile saline 70% alcohol.
    2. With a sterile syringe, aspirate the pus or exudate and transfer the pus into a sterile container.
    3. The pus may also be left in the syringe with needle stabbed into a rubber bung and transported immediately to the laboratory. This procedure is suitable is suitable for anaerobic culture.
    4. Send the specimen immediately to the laboratory. DO NOT STORE IN A REFRIGERATOR.
  1. 14 Tissue for C & S
    1. Collect tissue and aseptically transfer into a sterile container.
    2. Do not add fluid especially formalin solution.
    3. Send immediately to the laboratory.
  1. 15 Stool for C & S

Note: Bedpans for collecting specimens for culture should be sterile.

  1. Fresh stool:
  2. Using a swab collect a small amount of stool by dipping and rotating in the faeces taking care to include materials containing pus, mucus or blood if present.
  3. Places the swab with the stool into a sterile container screw the cap tighty and send it immediately to the laboratory
  4. If delay is unavoidable store at 4◦C <24 hours in respective ward.
  1. Rectal swab:

Note: Should only be taken if a stool specimen is not available. It is less satisfactory specimen than stool.

  1. Insert a sterile swab deep into the anus 1 inch beyond the anus sphincter so that the swab may come into contact with some faecal material. A satisfactory rectal swab is one which shows some faecal staining.
  2. Send the specimen to the laboratory as soon as possible. If not dip the rectal swab into the appropriate enteric transport medium as below:

Cary Blair Medium           :   suitable for most enteropathogenic bacteria

Selenite F Broth                 :   specifically for Salmonella sp.

Alkaline Peptone Water   :   for V. cholera and other vibrios.

                  

If specimen collection after office hours is unavoidable, store stool transport media in respective wards at RT.

  1. 16 High Vaginal Swab
    1. Wipe away excess amount of secretion/discharge.
    2. Obtain secretion from mucosal membrane of vaginal vault with sterile swab and send swab transport media.
  1. 17 Sputum for AFB Detection
    1. Sputum:
    2. Sputum is preferably collected when the patient first wakes up in the morning. Gargle mouth before sputum collection.
    3. Ask the patient to spit directly into a sterile container. Ensure that the expectorate is sputum and saliva.
    4. Send the specimen immediately to the laboratory. If delay is unavoidable store it in a refrigerator
  1. Other specimens:
  2. Collect specimens aseptically.
  3. Transfer into sterile bottle and send to the without delay. If delay is unavoidable store it in refrigerator.

         2. Serology

  • Blood collected in plain container should be allowed to clot by standing undisturbed at room temperature.
  • Clotted blood may then store at 4◦C if delay is unavoidable.
  • Each specimen should accompany by fully completed Microbiology request form.

         2.1 Collection of Specimen

For normal serologic and immunologic test:

  1. Aseptically collect 1-3 ml of blood (serum) into a plain container.
  2. Send the specimen to the serological laboratory immediately.

HBsAg, HbcAb, Anti-HBs, HIV and HCV Test

  1. Collect 5.0ml of blood into a plain container and allow to clot. Send the specimen to laboratory immediately.

          

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