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Microbiology 8
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LifeBridge Health - Department of Pathology

Microbiology

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, vaginal trap 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 needleb
Anaerobic transport system or capped syringe without needleb
Sterile 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 needleb
Sterile 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 needleb
Sterile 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 span
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 non-bacteriostatic 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
Bacterial Vaginosis Gram Stain for due cells from vaginal swab
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.