ACCEPTABLE SPECIMENS:
Respiratory specimen types: bronchial brush, bronchial wash, gastric aspirate (only pediatric patients), sputum (preferred), endotracheal aspirate/suction (ETA).

All other non-blood specimen types to include the following: abscess, bone marrow, CSF, peritoneal fluid, pericardial fluid, pleural fluid (pleural biopsy is preferred), skin lesion, synovial fluid, tissues, and wound aspirates.

Includes AFB Smear on respiratory specimen types. AFB smear may be requested on non-respiratory specimen types.

Causes for Rejection:
1. Specimen not labeled with patient's name, MRN #, date/time of collection, collector's initials. Specimen container leaking.
2. CSF when insufficient volume (<5 mL) received.
3. CSF specimen when cell count is normal (<=5 WBC/cubic mm, <20 WBC/cubic mm if newborn to 2 months of age) except from patients with HIV infection.
4. CSF specimen when cell count is indicative of bloody tap.
5. Nasal secretions & saliva are not acceptable.
6. URINE: Isolation of Mycobacteria from genitourinary tract is uncommon without a respiratory infection. If clinical reasons exist for culturing urine, contact the Infectious Diseases Service.
7. FECES: Isolation of Mycobacteria from feces is usually insignificant. If clinical reasons exist for culturing feces, contact the Infectious Diseases Service.

Collect specimens as follows:
RESPIRATORY SPECIMENS:
BRONCHIAL BRUSH:
1. Collect pulmonary secretions during bronchoscopy using a protected bronchial brush inserted through a special sterile cannula.
2. Submit brush in 1 mL of sterile saline in sterile screw top tube.

BRONCHIAL WASH:
1. Collect 2-5 mL of washing during bronchoscopy using sterile technique.
2. Submit in sterile screw top container.

GASTRIC ASPIRATE (pediatric patients):
1. Introduce nasogastric tube orally or nasally to stomach.
2. Perform lavage with 25-50 mL of chilled, distilled water or saline.
3. Before removing tube, release suction and clamp it.
4. Recover sample and submit in sterile screw top container.
NOTE: Collect specimen in early morning shortly after patient awakens in order to obtain sputum swallowed during sleep. Three specimens collected on successive days are desirable. Submit specimens collected AT LEAST 8 HOURS apart. Gastric Aspirate specimen must be in laboratory within 4 hours of collection.

SPUTUM - preferred over BAL:
1. Instruct patient to brush his/her teeth and/or rinse mouth well with water.
2. Have patient remove dentures.
3. Instruct the patient to take a deep breath, hold it momentarily, and cough deeply and vigorously into the container. Be sure patient understands the difference between sputum and saliva.
4. Collect 5-10 mL of sputum from an early morning, deep cough specimen or expectorated sputum induced by heated aqueous aerosol of 10% glycerin and 15% NACL in a screw-capped, sterile container.
NOTE: The specimen should be a single, first morning, "deep cough" sputum specimen, and the patient should not have eaten prior to collection. Three specimens collected on successive days are desirable. Submit 3 specimens collected AT LEAST 8 HOURS apart. When antibiotics are to be started immediately, a first morning specimen is still preferred.

OTHER NON-RESPIRATORY SPECIMEN TYPES:
BODY FLUID, BONE MARROW, SYNOVIAL FLUID:
1. Decontaminate skin with povidone iodine.
2. Aseptically aspirate fluid with needle and syringe. If fluid clotting is anticipated, collect with heparinized syringe.
3. Send fluid/bone marrow in a screw-capped, sterile tube or specimen cup.
NOTE: NEVER SUBMIT SWAB DIPPED IN FLUID. SUBMIT VOLUME OF FLUID.

CSF - preferred volume 10mL, minimum volume 5 mL:
1. Decontaminate skin with povidone iodine.
2. Perform sterile lumbar puncture; ventricular or suboccipital tap.
3. Send 10 mL or more (minimum volume = 5 mL) of spinal fluid in a screw-capped, sterile collection tube.
NOTE: CSF with normal cell count (<=5 WBC/cubic mm, <20 WBC/cubic mm if newborn to 2 months of

Anaerobic specimen containers (AS Tubes) transported via the pneumatic tube station are prone to breaking. Do not place more than one tube per bag. Additional packing material is recommended or considered sending via a courier.
DELIVER IMMEDIATELY TO MICROBIOLOGY IN A TIGHTLY SEALED STERILE CONTAINER WITH NO EXTERNAL SPILLAGE.
Gastric Aspirates MUST be received within 4 hours of collection.

Store specimens in refrigerator if transport will be delayed.

Causes for Rejection:
1. Specimen in leaking container.
2. Gastric Aspirates received more than 4 hours after collection.

Used to aid in the diagnosis of mycobacterial infections.

The Clinical Microbiology Laboratory Mycobacteriology Section provides definitive identification of mycobacteria to the species level and susceptibility testing for Mycobacterium tuberculosis complex isolates. The most rapid and reliable methods available for detection and identification of mycobacteria, especially M. tuberculosis, are used including fluorochrome stains for direct smears, BACTEC MGIT 960 for detection, and MALDI-TOF for identification.  Susceptibility testing is not routinely performed on non-tuberculous Mycobacteria.

Notes:
1. False negative results may occur when insufficient volume of fluid is cultured.
2. Few viable organisms may be present in a chronic lesion. The specimen must be large enough to permit recovery.
3. CSF volumes <5mL are suboptimal for the recovery of mycobacteria and are routinely not cultured.  CSF with normal cell count (<=5 WBC/cubic mm, <20 WBC/cubic mm if newborn to 2 months of age) are not routinely cultured. If clinical reasons exist for culturing in patient with normal cell count, contact the Clinical Microbiology Laboratory.
4. Isolation of Mycobacteria from genitourinary tract is uncommon without a respiratory infection. If clinical reasons exist for culturing urine, contact the Infectious Diseases Service.
5. Isolation of Mycobacteria from stool is usually insignificant. If clinical reasons exist for culturing stool, contact the Infectious Diseases Service.

Fluorochrome dye stain (AFB stain), Bactec Fluorescent Assay using MGIT 960 instrument and culture on solid media. 

Includes identification, and when appropriate, susceptibility testing at additional charges.

CPT coding cannot be determined before the culture is completed.