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Collection and Transport of Microbiology Specimens

Collection and transport of specimens for recovery of bacteria, chlamydia, mycobacteria, mycoplasma, ureaplasma, and fungi.

Abscesses, wounds, boils, pus, etc.

  • 1-5 mL  in anaerobe transport tube, vial or syringe with needle removed and capped. 
  • Tissue or exudate must be submitted.
  • Swabs are unacceptable. 
  • Collect with sterile needle and syringe. Expel air from syringe and inject into anaerobe tube, or cap the syringe.
  • If additional fluid is required to obtain specimen, use bacteristatic-free water. Swabs are generally not recommended because amount of specimen obtained is usually inadequate.  A portion of wall of abscess should also be included.

Blood Culture – See Blood Culture Collection Tab

Blood for Leptospira

  •  5 mL in sterile, heparinized tube
  •  Collect only during first 7 days of illness.
  •  After first 10 days of illness, urine should be cultured.

Bone

  • > 0.5 g in tube with small amount of Thioglycolate broth or in Petri dish.
  • Moisten specimen in Petri dish with small amount of sterile, nonbacteristatic saline. Do not send dry specimen. Each specimen should be accompanied by smear for gram stain. Multiple specimens are suggested.

Bone marrow

  • > 3-5 mL in syringe with heparin, or tube with 0.5 mL of 1:1,000 heparin.
  • Send capped, labeled syringe to lab or inoculate equally into aerobic broth and anaerobic blood culture bottles. If fungi are suspected, send only heparinzed bone marrow to lab.

Catheter, venous, arterial suction, drainage

  • Blood cultures should be collected at the same time.
  • Use sterile, specimen container
  • Disinfect area around entry site, remove catheter, and clip off tip aseptically into tube.
  • Send immediately to lab.  Do not send the line, only the tip.

Cutaneous skin for bacteria or fungi

  • Place skin scrapings in a sterile container.
  • Disinfect skin with 70% ethanol before obtaining scales with side of surgical blade or slide.  Specify for bacteria and/or fungi.

Cutaneous skin for virus culture

  • Use viral culturette swab or VCT medium
  • Collect and send moistened viral transport swab or medium to lab as early in day as possible.  Specify viral agent suspected.

Hair

  • Use sterile container.
  • Remove hair from infected area (preferably using a Wood's lamp) with forceps.
  • Removal of hair shaft is necessary. Send in taped Petri dish.

Nails

  • Use sterile container.
  • Disinfect nail surface with 70% ethanol. Scrape away outer portion and obtain scrapings from deeper, infected areas

Ear (acute otitis media)

  • Use 2 culturette swabs of pus from ear canal; syringe with needle aspirate of middle ear effusion.
  • Tympanocentesis and culture are usually not necessary, except in therapeutic failures and neonates. Nasopharyngeal specimens for culture are not recommended. Before needle aspiration clean canal and tympanic membrane surface with 70% ethanol povidone-iodine.

Exudates (transudates, drainages, ulcer) for bacteria, fungi or mycobacteria

  • 2-5 mL in anaerobic transport tube, vial or capped syringe.
  • Use 2 Culturette swabs and an anaerobic transport vial or tube only if there is an adequate amount of exudates to aspirate.
  • Collect with sterile needle and syringe.  Expel air from syringe and inject into anaerobe tube, or cap the syringe.
  • If additional fluid is required to obtain specimen, use bacteristatic-free water. Swabs are generally not recommended because amount of specimen obtained is usually inadequate.
  • A portion of wall  of abscess should be included.

Eye conjunctiva, keratitis

  • Use 2 culturette swabs.
  • For Chlamydia VCT Medium call (717) 851-2583 for York or (717) 337-5130 for Gettysburg.
  • Do NOT use swab with a wooden shaft.
  • Collect specimen before topical anesthetics are applied. Obtain drainage material on swab.
  • Corneal scraping, intra-ocular fluid aspiration, or biopsy may be required for detection of fungi.  Note: For Chlamydia, culture swab must be swirled in VCT Medium ASAP.

Eye corneal scrapings

  • Directly inoculate media whenever possible.
  • Call microbiology lab for assistance. Laboratory will provide media for direct inoculation, including chocolate agar and sheep blood agar.  York will also use inhibitory mold agar and sheep blood agar with CG, and SDA for fungus testing.

Feces, stool for bacteria

  • Stool transport device is available. Collect >1 gram stool in container for each type of study.  If transport delay is probable, put some of the specimen in transport media (Cary Blair Para-Pak). Send both samples. Raw stool should be refrigerated within 1-2 hours of collection or placed in a Para-Pak which is stored at room temperature.
  • Freshly-collected specimen is essential. If swab is used, it should be passed beyond anal sphincter, rotated carefully, and withdrawn. 
  • Three specimens often required for detection of bacterial pathogens. Not recommended for diagnosing intestinal mycobacteria infection. Biopsy culture more specific.

Fluid, abdominal (peritoneal, paracentesis, bile)

  • Collect > 10 mL specimen with a sterile needle and syringe. Expel air from the syringe. 
  • Either inject the fluid into an anaerobic transport device for anaerobes and a sterile specimen container for aerobes or remove the needed and send the capped syringe to the lab.  Specimen may also be collected in sterile vacuum bottles and sent to the lab.
  • An additional 5-10 mL should be submitted for each, if both mycobacteria and fungus cultures are desired.

Fluid, chest (pleural, thoracentesis, empyema)

  • Collect > 10 mL specimen with a sterile needle and syringe. Expel air from the syringe. 
  • Either inject the fluid into an anaerobic transport device for anaerobes and a sterile specimen container for aerobes or remove the needle and send the capped syringe to the lab.  Specimen may also be collected in sterile vacuum bottles and sent to the lab.
  • An additional 5-10 mL should be submitted for each, if both mycobacteria and fungus cultures are desired.

Fluid, pericardial

  • Collect 1-5 mL specimen with a sterile needle and syringe. Expel air from the syringe. 
  • Either inject the fluid into an anaerobic transport device for anaerobes and a sterile specimen container for aerobes or remove the needle and send the capped syringe to the lab.  Specimen may also be collected in sterile vacuum bottles and sent to the lab.
  • An additional 5-10 mL should be submitted for each, if both mycobacteria and fungus cultures are desired.

Fluid, synovial

  • 1-5 mL
  • Collect synovial fluid in syringe, then transfer to sterile, heparinized green top tubes.

Fluid, CSF

  • 1-5 mL each culture in sterile, screw-capped tube. When multiple tubes are collected, designate tube #2 for Microbiology. Deliver to lab immediately.
  • Disinfect skin carefully with povidone-iodine. Send specimen immediately to Microbiology Lab. At least 2 mL of additional CSF needed (each) for mycobacteria and fungus cultures.

Fluid, dialysate (peritoneal)

  • 50 mL in dialysate bag or sterile container.

Genitourinary for routine bacterial pathogens from cervix, culdocentesis fluid, penis, etc.

  • Use 2 culturette swabs. Anaerobic transport vial or tube for endometrial specimens only.
  • Anaerobe culture will not be performed unless specimen is received in anaerobe transport vial. If anaerobe infection of uterus is suspected, disinfect cervix and attempt to aspirate material through the cervical os. 
  • Expel air from syringe and inject specimen into anaerobe vial.

Genitourinary Culture for all sources other than endocervical or urethral

  • Use 2 culturette swabs.

Genitourinary for Streptococcus, Beta Group B Culture

  • Use 1 culturette swab

Genitourinary for Chlamydia Trachomatis and N. Gonorrhoeae Detection by DNA Amplification–Female and Male, > 13 years of age.  

Endocervical Swab Specimen Collection using BD ProbeTec ET CT/GC Amplified DNA

  • Assay Collection Kit for Endocervical Specimens.
  • Remove the cleaning swab from packaging.
  • Using the cleaning swab, remove excess mucus from the cervical os.
  • Discard the used cleaning swab.
  • Remove the collection swab from packaging.
  • Insert the collection swab into the cervical canal and rotate for 15-30 seconds.
  • Withdraw the swab carefully.  Avoid contact with the vaginal mucosa.
  • Uncap the CT/GC Diluent tube. 
  • Fully insert the collection swab into the CT/GC Diluent tube.
  • Break the shaft of the swab at the score mark.  Use care to avoid splashing of contents.
  • Tightly recap the tube.
  • Label the tube with the patient information and date/time collected.
  • Transport to the laboratory.

Male Urethral Swab Specimen Collection using BD ProbeTec ET CT/GC Amplified DNA

  • Assay Collection Kit for Male Urethral Specimens.
  • Remove the swab from packaging.
  • Insert the swab 2-4 cm into the urethra and rotate for 3-5 seconds.
  • Withdraw the swab.
  • Uncap the CT/GC Diluent tube
  • Fully insert the swab into the CT/GC Diluent tube.
  • Break the shaft of the swab at the score mark.  Use care to avoid splashing of contents.
  • Tightly recap the tube.
  • Label the tube with patient information and date/time collected.
  • Transport to the laboratory.

 Swab Storage and Transport

After collection, the endocervical swabs and the male urethral swabs must be stored and transported to the laboratory and/or test site at 2-27°C within 4-6 days.  Storage up to 4 days has been validated with clinical specimens; storage up to 6 days has been demonstrated with seeded specimens.

NOTE: If specimens cannot be transported directly to the testing laboratory under ambient temperatures (15-27°C) and must be shipped, an insulated container with ice should be used with either an overnight or 2-day delivery vendor.

Urine Specimen Collection

  • The patient should not have urinated for at least 1 hour prior to specimen collection.
  • Collect specimen in a sterile, plastic, preservative-free specimen collection cup.
  • The patient should collect the first 15-20 mL of voided urine (the first part of the stream, NOT midstream).
  • Label with patient identification and date/time of collection.

NOTE: During the clinical evaluation, testing urine volumes up to 60 mL was included in the performance estimates.  Specimens must be shipped in an insulated container with ice using either an overnight or 2-day delivery vendor.  Storage up to 4 days has been validated with clinical specimens; storage up to 6 days has been demonstrated with seeded specimens.

Genitourinary for Chlamydia Culture

  • For cases of rape or child abuse; genital swabs on children <12 yrs.; conjuctival specimens; rectal specimens; nasal washes; test of cure. 
  • 2 swabs in VCT media.
  • Both swabs should be swirled in the same vial of VCT media and the VCT media sent to the lab immediately or stored at 2-8°C up to 2 hours.

Genitourinary for Herpes simplex

  • Use viral culturette swab or VCT medium
  • Carefully open vesicular lesions. Blot fluid with dry swab. Fluid can be collected with small syringe and needle, expelling contents into transport medium (VCT). Collect cellular material by scraping base of vesicular/ pustular lesions with sterile scalpel blade and place in VCT.

Genitourinary for Ureaplasma

  • Use Mycoplasma Transport Medium.
  • Collect specimen as described above for Chlamydia. Bring to lab immediately or store in refrigerator <2 hr. Swab must be swirled in Mycoplasma Transport Medium (available from Microbiology Lab) as soon as possible.

 Respiratory tract, bronchial washings

  • 5 mL in Sterile, screw-capped container
  • Due to probability of oropharyngeal contamination, bronchial washings are not usually indicated for routine bacterial cultures.

Respiratory tract, gastric washings

  • 1.5 mL in sterile, screw-capped container.
  • Send to lab immediately. Send >5 mL (each) for fungal and mycobacteria cultures.

Respiratory tract, NP swabs

  • For B. pertussis or respiratory viruses, collect and submit nasopharyngeal flocked swab in UTM.
  • NP swabs are also used to detect carrier states for organisms such as C.diphtheriae or N.meningitidis

Respiratory tract, sputum (bacteria, mycobacteria, and fungi)

  • Use sterile specimen container.
  • 1.5 mL for routine bacteria; 5mL each for Mycobacteria or Fungi
  • Do not send salivia. If possible, have patient rinse mouth with water prior to collection.
  • Have patient cough deeply or induce coughing with heated aqueous aerosol of 10% glycerin and 15% NaCl. 5 mL samples (each) must be submitted (in addition) for recovery of mycobacteria and fungi. Obtain 3 successive early morning samples for TB and fungi.

Respiratory tract, throat (Group A Streptococcus)

  • Use culturette swab
  • Thoroughly swab right tonsil/fossa, move to right arch, uvula, left arch and left tonsil/fossa. Avoid swab contact with contaminated pharyngeal area. Sample areas of ulceration, exudation, or capsule formation.

Respiratory tract, throat (Mycoplasma pneumoniae)

  • Use swab in Mycoplasma transport media
  • Place swab into mycoplasma transport media.

Respiratory tract, throat (virus)

  • Use viral culturette or VCT medium.
  • Place swab back in Culturette casing (and moisten) or swirl in VCT. Specify viral agent.

Respiratory tract, tracheal aspirate    

  • > 1 mL in sterile screw-capped container.

Respiratory tract, transtracheal aspirate

  • 3-5 mL in anaerobe transport vial
  • Use sterile syringe to aspirate material from transtracheal catheter. Expel air and inject contents into anaerobe vial. Anaerobe culture will not be performed unless specimen is received in anaerobic container.

Surgical specimen, tissue biopsy, pus (for bacteria, mycobacteria, or fungi)

  • 0.5-5 gram or 1-5 mL Use anaerobic swab, vial or tube. Send in sterile screw-capped (aerobic) container if anaerobic culture is not necessary.
  • When possible, send multiple specimens from different sites. Abscess samples should include pus and part of abscess wall. Anaerobe culturing will not be performed if specimen is not received in anaerobic container. 
  • Obtain 2 biopsies when possible, one from wall or adjacent normal tissue and one from center of lesion. 
  • Do not send swabs.

 Urine, midstream or catheterized

  • 1-10 mL. B-D Urine Culture Kit requires >4.5 mL urine. <4.5 mL urine send in specimen container on ice.
  • >10 mL urine (each) will be necessary for mycobacteria and fungus cultures.
  • For recovery of mycobacteria or fungi, send 3 early morning samples.
  • Collection of midstream urine only after proper disinfection (followed by thorough rinsing) of area is essential. See collection instructions for clean catch midstream urine.
  • Single urethral catheterization is not recommended for collection of routine specimens from cooperative patients.
  • Indwelling urethral catheter specimen is collected by direct aspiration through the catheter wall using needle and syringe.
  • Do not obtain urine from the bag.  

Urine, suprapubic aspiration

  • 1-10 mL in B-D Urine Culture Kit or anaerobe vial
  • >5-10 mL urine (each) will be needed for mycobacteria and fungus cultures.
  • If anaerobic bacteriuria is suspected, expel air from syringe and expel contents into anaerobic transport vial. Anaerobe culture will not be performed if specimen is not received in anaerobic container.

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