Microbiology Specimen Collection Information

Test Code

ZMICRO

Preferred Specimen

Test Name	Synonyms	Specimen source	Patient preparation & Specimen Collection	Minimum Quantity	General Test Info	TAT
AFB Smear and Culture	Acid-fast bacillus, Mycobacteria, MAI, Acid-fast culture & smear, TB	Sputum, urine, bronchial washing, tissue, body fluid, wound	Collect before therapy. At least on specimen should be a first morning specimen. Sputum collection device or sterile container. For sputum see detailed collection in attachment A. Deliver immediately.	5-10 mL	Acid fast smear and culture to detect tuberculosis or mycobacterial infection	Smear results reported in 24-48 hrs. Positive cultures reported as soon as they become positive. Cultures incubated for 8 weeks.

AFB Blood Culture	Acid-fast bacillus, Mycobacteria, MAI	Blood	Collect before therapy. Follow Blood Culture Collection procedure using Myco/F Lytic bottle.	3-5 mL	Blood culture to detect tuberculosis or mycobacterial infection	Culture held 6 weeks. Positive cultures reported as soon as they become positive.

Anaerobic Culture		Body fluid, tissue, wound	Superficial material collected from skin surface, mucus membranes or edges of a wound are not acceptable. Prompt delivery is necessary to ensure minimum delay and prompt processing. Use anaerobic transport medium.		Anaerobic culture will only be done if specifically requested.	3 days

Chlamydia trachomatis culture	Trachoma	Genital, conjunctiva, NP	VCM transport medium.			Done Mon-Sat 3-5 days

CSF Gram stain and culture	Cerebrospinal fluid, spinal fluid culture	CSF	Sterile tube #2. Immediate delivery is necessary to ensure minimum delay and prompt processing.	1 mL	Purpose is to detect or rule out agents of bacterial meningitis. Smear for gram stain is included. AFB/Fungus requests must be ordered separately.	Gram stain: 1 hr Culture: 3 days

Cytomegalo-virus culture	CMV	1. bronchial washing or brushing, nasal washing or aspirate, first morning urine	1. In sterile leakproof container			Set up daily. 4-5 days
		2. throat swab	2. In VCM transport medium

Ear cultures		Ear	Culture swab or mini-tip or aspirate in sterile container		Do NOT refrigerate	2 days

Eye culture	Conjunctiva culture, corneal culture	Eye	Withhold topical antibiotic until specimen is collected. Conjunctiva - Mini-tip swab Aspirates - sterile leakproof container Cornea – Inoculate chocolate agar directly with spatula			2 days

Fluid culture	Body fluid culture	Peritoneal, pleural, paracentiesis, thoracentesis, synovial	Sterile leakproof container Prompt delivery is necessary to ensure minimum delay and prompt processing.	1 ml		3 days

Fungus culture	Fungal culture, mycology culture, yeast culture	Any source	Refer to attachment A for collection of hair, skin or nails. Collect before therapy. Sterile container or swab	1 ml		Held 4 weeks, positives reported as soon as results are available

Fungus Blood Culture		Blood	Collect before therapy. Follow Blood Collection Procedure using Myco/F Lytic	3-5 ml		Culture held 4 weeks

Fungus smear		Sources other than hair, skin or nails. See KOH prep for hair, skin or nails.	Sterile leakproof container or swab in transport medium		Detects yeast, fungal elements	1 day

Genital culture		Vagina, cervix urethra, placenta	Swab in transport medium		Aerobic culture only.	3 days

Giardia antigen		Stool	stool in 10% formalin or Cary Blair	5 gm		M-F 3 days

Gonococcal culture	GC screen, gonorrhea screen, Neisseria gonorrhoeae culture	Urethra, vagina, cervix, pharynx, conjunctiva	Swab plated directly on Martin-Lewis agar or in transport medium delivered immediately to laboratory		GC is susceptible to cold and drying. NAAT tests such as TMA or SDA are preferred.	3 days

Influenza PCR	flu PCR	Nasopharyngeal swab, throat swab, bronchial wash or aspirate, sputum	VCM transport	1 mL		1-2 days

KOH prep	fungus smear, calcofluor stain	Hair, skin, nails			Direct exam for fungus	1 day

IV catheter tip culture	cath tip culture	IV catheter tip or segment	Collect aseptically according to nursing procedure and submit in a sterile container			3 days

Mycoplasma pneumonia culture	L-forms, PPLO	Respiratory sources	Submit in VCMTransport Medium available in laboratory. Do not use wooden shaft swabs, they may be toxic to mycoplasmas.		Mycoplasma is sensitive to drying. Specimen must be put in transport immediately. Source is important as to which Mycoplasma is sought. Ureaplasma (prev. T-strain Mycoplasma) is common in the genital tract and should be ordered as Ureaplasma culture.	2 weeks – prelim 5 weeks – final

Parasite ID	Worm identification	Worm, tick, lice	Sterile container			2 days

Pertussis PCR	Bordetella pertussis, whooping cough	Nasopharyngeal	Nasopharyngeal swab: Use E-swab or Amies' collection tube with liquid Amies and wire collection swab. Do not use calcium alginate swabs, as they may contain substances that inhibit PCR.		Includes PCR for B. pertussis & B. parapertussis	Mon-Fri 1-3 days

Pinworm	Cellophane tape test, Enterobius vermicularis, Scotch tape prep	Perianal	Collect one pinworm “paddle" consisting of a clear plastic spatula with adhesive on one side. Press gently onto the folds of the perianal area. Clear cellulose tape on a glass slide is also an Acceptable sample type. Collect specimen first thing in the morning.		Send specimen at room temperature. Stool specimens and frosted tape preparations will be rejected.	3 days

Stool culture		Stool, rectal swab	CaryBlair transport medium. Rectal swab in Cary Blair or Amies transport medium Inpatient within 3 days of admission. Outpatient up 3 specimens collected on different days.	1 gm	Detects: Aeromonas, Campylobacter, Pleisiomonas, Salmonella, Shigella, Yersinia, and Vibrio. Must specifically request E.coli O157 if desired.	4 days

Stool for Shiga toxin	STEC	Stool	CaryBlair transport medium.	2 gm		M, W, F 3 days

Mycobacterium tuberculosiscomplex Direct Detection by TMA	TB TMA	Sputum, bronchial wash/brush, tracheal aspirate	Sterile leakproof container	3 mL		M-F 4 days

Tissue culture		Biopsy, surgical specimen	Sterile container		Anaerobic cultures must be specifically requested. If fungus & AFB cultures are required they must be specifically requested.	3 days

Ureaplasma culture	Mycoplasma T-strain	Urogenital swab, respiratory specimens, sterile body fluids, tissue	Submit in VCM transport medium. DO NOT use wooden shaft swabs or cotton swabs Ureaplasmas and mcoplasmas are extremely sensitive to adverse environmental conditions, particularly drying, osmotic changes, toxic metabolites, and temperature fluctuations			10 days

Urine culture		Urine Specify if clean catch, in/out cath, indwelling cath, suprapubic, cystoscopic, or kidney	Collect before antibiotic administration in a sterile container. Deliver promptly or refrigerate.	0.5 ml	Specimens from a catheter bag and Foley cath tips are not acceptable. Place urine into urine culture transport tube immediately or refrigerate if not transported to the laboratory within 30 minutes.	1-2 days

Virus culture		Specify source on the order	Fluids in sterile container, swabs in VCT	nasal wash/ aspirate 3mL, other 1 ml	Call lab for VCM. Must specify which viruses to be cultured.	Varies with virus (up to 2 weeks)

Instructions

Source	Detailed Collection Information
Sputum	Sputum should be the result of a deep cough (not saliva) the first thing in the morning if practical or should be induced by an aqueous aerosol. Have patient remove dentures and rinse mouth with water. Collect 5 to 10 ml directly into a sterile container. Deliver to the laboratory within 1 hour. Refrigerate if can not be delivered immediately.
Tissue, Biopsy, or Bone	Collect tissue aseptically from the center and edge of the lesion. Collect bone aseptically. Place specimen between moist gauze squares, add a small amount of sterile water or sterile non-bacteriostatic 0.85% saline to keep tissue from drying out, and send immediately to the laboratory. Do not refrigerate.
CSF	Collect as much spinal fluid as possible, and place it in a sterile leakproof container. At least 1 mL is needed for Gram stain and culture. AFB and fungus culture require an additional minimum of 3 mL each. Generally, the no. 3 tube is used. Do not refrigerate. Deliver to the laboratory immediately.
Body fluids (pleural, synovial, and peritoneal)	Collect specimens aseptically, and place them in sterile leakproof containers. Do not refrigerate. Transport to the laboratory immediately.
Hair	Use a forceps to remove at least 10 infected hairs. Place hairs in a dry, sterile tube or container.
Nail	Remove nail polish from the nail to be sampled. Clean nail with 70% alcohol. For a specimen of the dorsal plate, scrape the outer surface of the nail and discard the scrapings. Then scrape the deeper affected portion of the nail to obtain the specimen. Remove a portion of debris from under the nail with a scalpel. The whole nail or nail clippings may also be submitted. Place all material in a dry, sterile tube or container.
Skin and interspaces	Clean the skin surface with 70% alcohol. Scrape the surface of the skin at the active margins of the lesion(s) with a sterile scalpel. Place scrapings in a dry, sterile tube or container.

The CPT Codes provided in this document are based on AMA guidelines and are for informational purposes only. CPT coding is the sole responsibility of the billing party. Please direct any questions regarding coding to the payor being billed. Any Profile/panel component may be ordered separately. Reflex tests are performed at an additional charge.