Microbiology 8 - Baltimore Maryland MD

Craig R Suchin, M.D. Dept of Radiology , Diagnostic Radiology, Board Certified

Debra Freeman, M.D. Emergency Department , Pediatrics, Board Certified

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Microbiology 8

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Microbiology

Microbiology 8

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LifeBridge Health - Department of Pathology

Microbiology

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Table 3 Specimen transport guide

Source and type of specimen	Transport method

Blood	Blood transport system or sterile tube with SPS. If Neisseria spp. are suspected, use transport system without SPS.

CNS CSF Ommaya fluid Brain abscess CNS biopsy	Sterile screw-cap tube Sterile screw-cap tube Anaerobic transport system Anaerobic transport system. If specimen is small send in sterile cup with small amount of nonbacteriostatic 0.85% NaCl. (Never place in formalin.)

Gastrointestinal system Feces Rectal swab Gastric lavage or washings Duodenal aspirate	Sterile screw-cap cup; tube with Carey Blair medium or buffered glycerol saline Swab transport system (For pinworm, use pinworm collection kit.) Sterile screw-cap cup or sputum trap

Rectal biopsy Sigmoidoscopy specimen	Sterile screw-cap cup or sputum trap Sterile screw-cap cup or tube. If specimen is small, send in sterile cup with small amount of nonbacteriostatic 0. 85% NaCl. (Never place in formalin.) Sterile screw-cap cup or tube. If specimen is small, send in sterile cup with small amount of nonbacteriostatic 0.85% NaCl. (Never place in formalin.)

Eye Conjunctival scrapings Corneal scrapings Intraocular fluid	Send prepared smears and directly inoculated media Send prepared smears and directly inoculated media Send prepared smears and directly inoculated media, anaerobic transport system, or capped syringe without needle with air expelled.

Genital tract, female Amniotic fluid Fallopian tube Bartholin fluid Cervical Swab Urethral Swab Vaginal Swab Endometrial Vulval	Anaerobic transport system with 1-2 ml of sample Anaerobic transport system with 1-2 ml of sample Anaerobic transport system with 1-2 ml of sample Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system Sterile screw-cap cup or tube or anaerobic transport system Capped syringe without needle; slide with coverslip for T. pallidum; swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system

Genital tract, male Anal swab Urethral Swab Epididymis Prostatic massage Semen Penile lesion	Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system Anaerobic transport system, sterile screw-cap cup Sterile screw-cap cup, tube or swab transport system Sterile screw-cap cup, tube or swab transport system Capped syringe without needle; slide with coverslip for T. pallidum; swab transport or viral or chlamydial transport system

Specimens for N. gonorrhoeae Anal, cervical, urethral, vaginaltrap or sterile screw-cap cup or tube	Swab transport system; direct inoculation to MTM, ML, or New York City agar; N. gonorrhoeae transport system

Lower respiratory tract Lung biopsy Expectorated sputum Induced sputum Tracheal or endotracheal aspirate	Sterile screw-cap cup; if specimen is small, place it in a small amount of nonbacteriostatic 0.85% NaCl (never place in formalin) Sterile screw cap cup Sterile screw-cap cup Sputum trap or sterile screw-cap cup or tube

Lower respiratory tract (cont.) Bronchoalveolar lavage fluid Bronchial washings Transbronchial biopsy Bronchial brush Transtrachial aspirate Lung aspirate	Sputum trap or sterile screw-cap cup or tube Sputum trap or sterile screw-cap cup or tube Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Anaerobic transport system or sterile screw-cap cup or tube Anaerobic transport system or sterile screw-cap cup or tube

Upper respiratory tract Throat swab Nasal swab Oral culture Nasopharyngeal swab Tympanocentesis fluid Sinus aspirate Nasopharyngeal suction Nasal washings	Swab transport or virus transport system Swab transport or virus transport system Swab transport or virus transport system Swab transport or virus transport system Anaerobic transport system or capped syringe without needle^bAnaerobic transport system or capped syringe without needle^bSterile screw-cap cup or viral transport system Sterile screw-cap cup or viral transport system

Sterile body fluids (excluding CSF, urine, blood) Pleural, peritoneal, ascites, joint and synovial fluids	Sterile screw-cap container, capped syringe without needle, or anaerobic transport system

Subcutaneous tissue and skin Ulcers or nodules, superficial wound (bacterial) Exudate Biopsy Burn specimens Superficial fungal lesion material	Capped syringe without needle^bSterile screw-cap cup (If specimen is small, place it in a small amount of nonbacteriostatic 0.85% NaCl to prevent drying.) Sterile screw-cap container Sterile screw-cap container

Deep wounds, aspirates, tissues Site wound Deep wounds or abscesses Soft tissue aspirates Bone Punch skin biopsy	Anaerobic transport system Sterile screw-cap container Capped syringe without needle^bSterile screw-cap container (If specimen is small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent drying.) Sterile screw-cap container (If specimen is small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent drying.)

Urine Clean catch Ileal conduit Straight catheter Suprapubic aspirate Bladder washout Bilateral ureteral catheterization	Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube Anaerobic transport system or capped syringe without needle Sterile screw-cap cup or tube (Be careful to label specimens with correct times and sites) Sterile screw-cap cup or tube (Be careful to label specimens with correct times and sites.)

^a Refer to Table 1 for anaerobic transport systems and to Table 2 for swab transport and N. gonorrhoeae transport. Abbreviations: MTM: modified Thayer-Martin; ML: Martin-Lewis.
^b Specimens obtained by a physician using needle aspiration should be transferred to a sterile tube or an anaerobic transport vial prior to transport of the specimen to the laboratory. If there is little material in the syringe, the physician should draw a small amount of sterile nonbacteriostatic 0.85% NaCl or sterile broth through the syringe and then transfer the specimen to a sterile tube. Alternatively, and only if the specimen will be compromised by transferring it from the syringe, a small amount of sterile O.85% NaCl or broth may be draw into the syringe prior to removal of the needle. The physician should use a protective device while removing the needle to avoid injury and should cap the syringe with a sterile cap prior to transporting it to the laboratory.

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Table 4 Collection considerations for CNS specimens

Culture	Vol. (ml)	Comments
Bacteria	1 ml	Send cloudiest CSF to micro lab ASAP, tube #2 preferred
Fungi	2 ml	Rule out Cryptococcus spp., Coccidioides immitis
Mycobacteria	2 ml	M. tb., M. avium-intracellularae
Anaerobes	NA	Brain abscess or CNS biopsy specimens
Parasites	NA	Brain abscess or CNS biopsy specimens for E. histolytica, Toxoplasma gondii, Naegleria sp., Acanthamoeba spp.
Virus	1-2 ml	Send to laboratory on ice. Sent to reference lab.

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Table 5 Collection considerations for gastrointestinal specimens

Culture	Comments
Bacteria	Stools: Three stools on three separate days recommended. Gram stain for fecal leukocytes only. Gastric biopsy: Rule out Helicobacter pyloriRectal swab: Rule out enteric pathogens (esp., Shigella), and GC
Fungi	Gastric aspirate, gastric biopsy, esophageal rush, esophageal biopsy.
Pinworm	Swab perianal area when patient gets up in the morning before patient bathes or defecates. See Parasitology manual for specific instructions.
Mycobacteria	Gastric aspirate or gastric biopsy; feces
Parasites	If transport to laboratory is delayed, place stool specimen in preservative. Duodenal aspirates are useful for detecting Giardia spp. and larvae of S. stercoralis and A. lumbricoides. Use rectal biopsy specimens for E. histolytica and E. coli Use small bowel biopsy specimens for Giardia, Cryptosporidium, and Microsporidium
Virus	Esophageal specimens for CMV and HSV and rectal biopsy specimens for HSV. Send to lab in appropriate media. Do not freeze specimens for viral culture.

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Table 6 Collection considerations for genital tract specimens

Culture	Recommended specimens
N. gonorrhoeae	Cervical, urethral, anal, or vaginal swabs.
Bacteria	Prostatic fluid, cervical, vaginal
Trichomonas vaginalis	Vaginal, prostatic fluid
Fungi	Anal, vaginal, or cervical
Anaerobes	Epididymis aspirate, amniotic fluid, abscess fluid
HSV	Genital or perianal lesion
C. trachomatis	Urethral, vulval, cervical
T. pallidum	Genital lesion. Secondary lesions of syphilis are commonly found on mucous membranes and skin, but any body organ may be involved.
U. urealyticum	Urethral, epididymis, or prostatic fluid
LGV	Rectal, cervical, urethral, bubo or ulcer material
H. ducreyi	Material from ulcers of genitalia and perianal areas and from inguinal nodes.

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Table 7 Collection considerations for ocular specimens

Culture	Comments
Bacteria	Inoculate media directly with ocular scrapings. (If GC is suspected, inoculate a TM or GC lect plate.
Fungi	Inoculate media directly with ocular scrapings.
Anaerobes	Use anaerobic transport medium, or inoculate medium directly. If inflammation occurs after extracapsular cataract extraction, rule out Proprionibacterium spp.
Parasites	Use to detected Acanthamoeba spp.
Chlamydia	Do not use cotton swabs for specimen collection.
Virus	Do not use calcium alginate swabs for specimen collection.
Mycobacteria	Inoculate medium directly with ocular scrapings.