Special notes from Microbiology
All microbiology specimens must be collected with sterile swabs or in sterile containers.† All unpreserved specimens, such as urine, sputum, tissue, CSF and other body fluids must be promptly delivered to the laboratory or refrigerated if delivery is delayed over 1 hour.
Acid fast culture and smear
††††††††††††††††† Sputum:† Specimens must be collected in the sputum containers available through SMART.† Specimens submitted for AFB culture in other containers will be rejected.
††††††††††††††††† Urine:† The first voided specimen in the morning collected in a sterile container.† 24-hour specimens are not accepted.
††††††††††††††††† Note:† Acid fast smears are done on all specimens.† Specimens received in the laboratory before 10:00 will have the smear reported by 1530.† Cultures are sent to Kansas Department of Health Laboratory and incubated 6 weeks before a final negative report is issued.
Anaerobic cultures will be included on all appropriately collected and transported surgical specimens, deep wounds and body fluids.† Aspirations are preferable to swabs.† Aspirations may be submitted in a capped syringe or sterile leak proof container; swabs should be submitted in anaerobic transport tubes that are available from the Microbiology laboratory.† The same specimen may also be used for aerobic culture.
Culture samples should be collected so as to avoid contamination with indigenous anaerobic flora from skin and mucous membranes.† Because of large resident anaerobic flora, the following sites are inappropriate for anaerobic cultures:† throat, nasopharynx, sputum, urine, urogenital tract, and superficial wounds.†
To avoid skin flora contamination the phlebotomy site must be prepared with a one-minute chlorhexidine gluconate (CHG) scrub, which is allowed to dry.† Cultures are incubated for five days before final results are reported.† If Brucella is suspected, the Microbiology Laboratory must be notified so that cultures will be held for 30 days.† If fungus or mycobacterium is suspected, order as a Fungus blood culture or an AFB blood culture.
Obtain with culture collection swabs.† Culture for gonorrhea is included.† These specimens are not appropriate for anaerobic culture do to large resident anaerobic flora.
††††††††††††††††††††††† Transport media and swabs are available in the Microbiology Laboratory.† To be ordered for genital specimens on children under 12 and for specimens other than cervix, urethral or urine.
Chlamydia and/or Gonorrhoea DNA
††††††††††††††††††††††† Collection kit with instructions for collection are available through SMART.† Specify site (cervix, urethral or urine only). Use ProbeTec swabs only. Use the large swab to clean the mucous from the cervix. Then collect the sample by inserting the small swab into the cervical canal and rotate 15-30 seconds. For male urethral collection, use the male ProbeTec collection swab. Insert the swab 2-4 cm into the urethra and rotate 3-5 seconds. For urine specimens, collect the first 15-20 ml of voided urine, not midstream. Specimens may be transported to the lab at room temperature. Bloody specimens and specimens contaminated with mucous should be avoided. Blood and mucous are inhibitory to the test.
††††††††††††††††††††††† Collection kit and instructions for specimen collection are available from the Microbiology Laboratory.† To be ordered for nasopharyngeal specimens on neonates and on specimens from eyes.
Clostridum Difficle Toxin
††††††††††††††††††††††††††††††† Submit stool specimens to the laboratory in round plastic, sealed containers available through SMART.† Specimens that are extremely small in quantity or dried up are unsatisfactory and will be rejected.† Swabs are not accepted.
Fungus smears and cultures
††††††††††††††††††††††† Microbiology personnel will collect skin scrapings, nail and hair clippings for culture and KOH examination.† Other specimens should be submitted in a sterile container or on a culture collection swab.† Cultures will be incubated for four weeks before a final negative report is issued.† Urine:† The first voided specimen in the morning collected in a sterile container.† 24 hr specimens are not accepted.
Miscellaneous body site
††††††††††††††††††††††† (Wound, abscess, ear, eye, fluids, tissue, endometrial, placenta, Bartholin cyst)
††††††††††††††††††††††† Small volumes of fluid (less than or equal to 10 ml) can be submitted in a syringe.† Remove needle and cap syringe before transporting.† Larger volumes (greater than 10 ml) can be submitted in a sterile container.† Tissue in formalin will be rejected. Culture collection swabs may also be used. Anaerobic culture will be included if collected appropriately from a normally sterile site.
Respiratory cultures - lower
††††††††††††††††††††††† (Sputum, bronchial washings and brushing, lung biopsy, ET tubes, and tracheal suction material)
††††††††††††††††††††††† Sputum specimens are collected in the sputum containers available through SMART.† Tissue is collected in a sterile urine container.† Material obtained by suction can be collected in a sterile mucous specimen trap or other sterile suction tubes.
††††††††††††††††††††††† Sputum specimens that upon microscopic examination have greater than 10 epithelial cells per 100X low power field, represent saliva and will be rejected.†
Respiratory cultures - upper
(Nose, throat, nasopharyngeal)
††††††††††††††††††††††† These specimens are collected by phlebotomy personnel with a culture collection swab that contains a transport media.† Dry cotton swabs are not suitable and will be rejected if another specimen can be obtained.
††††††††††††††††††††††† No more than two specimens, one per day will be accepted.† Stool cultures should not be ordered on patients hospitalized over 3 days.† All specimens are routinely cultured for Salmonella, Shigella, E.coli 0157 and tested for Campylobacter antigen.† The Microbiology Laboratory must be notified if cultures for Yersinia or Vibrio cholera are requested. Specimen may be passed into a bedpan or stool specimen collector and transferred within one hour to a Para-Pak C&S preservative tube available from microbiology laboratory.† † Rectal swabs are to be submitted on a culture collection swab.† Specimens that are extremely small in quantity or dried up are unsatisfactory and will be rejected.† For patients over 6 months of age with clinically significant diarrhea and a history of antibiotic exposure, consider clostridium difficle toxin testing.
Stool exam for ova and parasites
††††††††††††††††††††††† No more than three specimens, one per day will be accepted.† If patient hasnít been out of the area consider ordering Giardia antigen test.† Ova and parasites should not be ordered on patients hospitalized over 3 days.† Specimen may be passed into a bedpan or stool specimen collector and transferred within one hour to an Ecofix preservative tube available from Microbiology Lab.† Stool that have been in contact with water or urine are not acceptable.
Urine culture with colony count
††††††††††††††††††††††† Follow the clean voided midstream method of specimen collection.† Patients must be thoroughly instructed on how to cleanse the urethral area and collect a midstream specimen.† Specimens must be collected in a sterile urine container† No more than one hour should elapse between the time the specimen is obtained and its arrival in the Laboratory.† If this time schedule cannot be followed, the urine specimen must be refrigerated immediately† Urine is not satisfactory for culture if it has been refrigerated for longer than 25 hours.† Specimens that are not submitted in a sterile container will be rejected unless another specimen cannot be obtained.