Specimen Collection and Handling Procedures Bacteriology Section

It is recommended that a pure isolate of the unknown organism be submitted for identification. This prevents delay in the identification of the organism. Submit the organism in thioglycolate, chopped meat or other growth supporting media. Avoid sending plates. Clinical material will be accepted but is not recommended due to the poor survival rate of the bacteria.

Clostridium difficile and Clostridium botulinum
Isolation and identification of pure isolates from clinical material is provided. Toxin testing is referred to the Centers for Disease Control and Prevention. Please call for instructions prior to submitting these specimens or in the case of suspected botulism.

Bacteria Identification
Submit a pure isolate of the unknown bacteria for identification. Please provide prior laboratory results, i.e. gram stain, growth requirements, organism suspected etc. Serological typing for Haemophilus influenzae and grouping for Neisseria meningitidis is performed. Submit isolates on appropriate growth supporting media in screw-capped tubes. Avoid sending plates.

Bordetella pertussis
Nasopharyngeal swabs are the specimens of choice. The Health and Environmental Testing Laboratory provide transport media and swabs.

  • Obtain a nasopharyngeal swab
  • Insert the swab into the culture tube of Regan-Lowe media, either cut the wire (even with the top of the tube) or fold the wire down into the tube.
  • Cap, label, and place in the plastic container.
  • Place the plastic container into the box provided and mail

Collect a freshly passed stool, uncontaminated by water or urine. Pick a portion of the stool with the swab provided and place into the vial of media. Leaving the swab in the vial, carefully break the swab at cap level. Screw the cap on tightly. Fill in the lab slip completely and forward these in the container provided. Stools for isolation and identification are accepted if submitted in appropriate transport systems. Chocolate agar slants are appropriate medium for submitting pure isolates for identification.

Pure isolates for identification are accepted. Clinical material submitted in a suitable transport system, i.e. culturette is also acceptable. Please call prior to the submission of specimens.

DNA probe testing for Neisseria gonorrhoeae and Chlamydia trachomatis
1. Unisex Swab Specimen Collection Instructions:
a. Endocervical swabs: Remove excess mucus from the cervical opening and surrounding mucosa using the cleaning swab (white shaft). Discard the swab.
b. Insert the specimen collection swab (blue shaft swab) into the endocervical canal.
c. Rotate the swab for 10-30 seconds for adequate sampling.
d. Withdraw the swab carefully; avoid any contact with the vaginal mucosa.
e. Immediately place the swab into the GEN-PROBE transport tube.
f. Break the swab shaft at the score line.
g. Re-cap the tube tightly.
h. Store the specimens at 2-30°C until shipped at this temperature to arrive at the laboratory within 60 days of collection.
2. Urethral swab specimens:
a. Patient should not have urinated for at least 1 hour prior to sample collection.
b. Insert the specimen collection swab (blue shaft swab) 2-4 cm into the urethra using a rotating motion to facilitate insertion.
c. Once inserted, rotate the swab gently using sufficient pressure to ensure the swab comes into contact with all urethral surfaces. Allow the swab to remain inserted for 2 to 3 seconds.
d. Withdraw the swab and place the swab into the GEN-PROBE transport tube.
e. Break the swab shaft at the score line.
f. Re-cap the tube tightly.
g. Store the specimens at 2-30°C until shipped at this temperature to arrive at the laboratory within 60 days of collection.
3. Urine specimen:
a. The patient (male or female) should not have urinated within one hour prior to providing the sample.
b. Direct patient to provide a first morning catch urine (20 to 30 ml of the initial voided urine stream) into a standard urine collection container, without preservatives. Collection of larger volumes of urine may result in specimen dilution that may reduce test sensitivity. Female patients should not cleanse the labial area prior to providing the specimen.
c. Remove the cap and transfer 2 ml of urine into the urine transport tube using the disposable pipette provided. The correct volume of urine has been added when the fluid level is between the black fill lines on the urine specimen transport tube label.
d. Re-cap the urine specimen transport tube tightly. This is now known as the processed specimen.
e. Store the processed urine specimens at 2-30°C until shipped at this temperature to arrive at the laboratory within 30 days of collection. 

Isolates from clinical, food or environmental specimens should be submitted on agar slants, for identification and serotyping. Serotyping is currently done at no charge to the submitter.

E.coli: 0157:H7
Stools, shiga toxin positive broths as well as pure isolates of E. coli are accepted for isolation, identification and serotyping.

Neisseria gonorrhoeae
FA reference slides and cultures are accepted. If warranted, identification and beta lactamase testing are done from culture. Submit viable cultures on appropriate media in a CO2 atmosphere.

Parasitic diseases
The laboratory no longer routinely provides this service. Please call for assistance during outbreaks or in identifying unusual parasites. Blood parasites are referred. Prior notification is necessary before submission of specimens to the Health and Environmental Testing Laboratory.