Gram stains are automatically performed on fluids and exudates
other than blood and urine. Do not send sterile body fluids in
plastic red top tubes. These tubes contain a clot activator which may
make testing unreliable.
Label transport tube with two patient identifiers, date and
time of collection. Transport at room temperature unless otherwise
A. Abscess - Tissue or aspirates are always superior to swab
specimens. Remove surface exudate by wiping with sterile saline or
70% alcohol. Aspirate with needle and syringe. Cleanse rubber
stopper of anaerobic transport vial (59546) with alcohol; allow to
dry 1 min before inoculating; push needle through septum and inject
all abscess material on top of agar. If a swab must be used, pass
the swab deep into the base of the lesion to firmly sample the
fresh border. Transport time ≤2 hours.
B. Anaerobic cultures - Tissue or aspirates are preferred
rather than swabs. Fluid collections should be aspirated through
disinfected tissue or skin. For superficial ulcers, collect material
from below the surface (after surface debridement or use a needle
and syringe). Submit specimens using anaerobic transport media:
a. Anaerobic transport vial (fluid specimen, 59546): Cleanse rubber
stopper with alcohol; allow to dry 1 min before inoculation;
push needle through septum and inject specimen on top of agar.
b. Anaerobic jar (tissue specimen, 59547). Place sample on top of
agar. Keep jar upright to maintain atmosphere in jar.
c. A sterile container (37777) may be used for tissue if
transported to the microbiology lab immediately (add drops of
sterile saline to keep small pieces of tissue moist).
d. Copan Liquid Amies Elution Swab (ESwab) (74541) - swab specimens
are suboptimal, but will be accepted if no other sample can be
e. Deliver all specimens to the laboratory immediately after
f. Anaerobic flora is prevalent on mucosal surfaces of the oral
cavity, upper respiratory, gastrointestinal, and genital tracts;
specimens collected from these sites should not ordinarily be
cultured for anaerobic bacteria. The following is a list of
specimens that are likely to be contaminated with anaerobic
normal flora and are NOT routinely accepted for anaerobic
1) Throat or nasopharyngeal swabs
2) Gingival or other intraoral surface swabs
3) Expectorated sputum
4) Sputum obtained by nasotracheal or endotracheal suction
5) Bronchial washings
6) Voided or catheterized urine
7) Vaginal or cervical swabs
8) Gastric and small bowel contents (except for "blind loop" or
bacterial overgrowth syndrome)
9) Feces (except for specific etiologic agents such as
C. difficile and C. botulinum)
10) Rectal swabs-Surface swabs from ulcers and wounds(collect
material from below the surface)
11) Material adjacent to a mucous membrane that has not been
a. Adult - Cleanse oil or visible dirt from site with
alcohol pads before using ChloraPrep skin prep. Cleanse skin with
ChloraPrep® one-step 1.5 mL Frepp®
1) Holding the applicator sponge downward, pinch wings on
applicator to break ampule and release the antiseptic.
2) Use a side-to-side motion to scrub the site with the friction
pad for a full 30 sec; allow site to dry completely (at least
30 sec) before venipuncture. Do not touch site after prep.
3) Remove overcaps from bottles (1 aerobic 924171 and 1 anaerobic
924172) and cleanse each rubber septum with separate 70%
alcohol swabs. Allow septum to dry for 1 min before
4) Draw 20 mL of blood and inoculate each bottle with 10 mL of
blood. Do not vent or overfill bottles. Adding low (<8 mL)
or high (>10 mL) volumes may adversely affect the recovery of
organisms. Transport time <2 h.
5) For adults with a suspected bloodstream infection (BSI),
collect two initial sets of blood cultures sequentially from
separate phlebotomy procedures followed by a third set at 4-6
hour intervals (will detect >98% of BSIs). A single set of
blood cultures to detect BSIs in adults is inadequate (only
73% sensitivity); two sets of blood cultures will allow
detection of 87.7-89.7% of BSI episodes. (J Clin Microbiol
6) If patient is allergic to chlorhexidine, prep site with a
povidone iodine swab stick (907172) applied in concentric
circles (start at center). Allow to dry at least 1 min before
venipuncture. If patient is allergic to iodine, cleanse site
with 70% alcohol for 60 sec.
b. Pediatric - Apart from NICU patients, the minimum volume
drawn should be 1 mL per year of age per blood culture set. This
volume should be split between an aerobic and anaerobic bottle.
See pediatric blood culture order for more detail.
D. Bone marrow aspirate - Prepare puncture site as for surgical
incision. Inoculate blood culture bottle (924171) or Isolator
(lysis centrifugation) tube (922848). Transport time <2 hours.
Routine bacterial culture of bone marrow is rarely useful.
E. Burn - Clean and debride burn. Place tissue in sterile screw-
cap container (37777). Transfer aspirates to a sterile container.
These are processed for aerobic culture only. Quantitative culture
may or may not be valuable. A 3 to 4 mm punch biopsy specimen is
optimum when quantitative cultures are ordered. Cultures of surface
samples can be misleading.
F. Catheter Tips - Catheter tips are not routinely accepted for
culture. Consult Microbiology laboratory for approval (pager 4903
weekdays; pager 3404 evenings and weekends). Foley catheters are not
accepted for culture since growth represents distal urethral flora.
G. Cerebrospinal Fluid (CSF) - Obtain CSF for gram stain, cell
count, protein, glucose and aerobic culture where able. Obtain kit
922257 (20G needle) or 922258 (22G needle) from Hospital Stores
356-1784). The kit should contain 4 pre-numbered tubes to be filled
in chronological order. Avoid covering tube numbers with
stickers to ensure appropriate routing of samples.
• With low volume, one-tube specimens not all testing may be
possible and the clinician must determine which tests should be
prioritized. If cultures are desired, Microbiology must receive
the specimen first to ensure the culturing of a sterile specimen.
• Transport time <15 minutes. Do not refrigerate CSF
for bacterial culture.
H. Decubitus ulcer - A swab is not the specimen of choice.
Cleanse surface with sterile saline. Submit tissue or aspirate
inflammatory material from the base of the ulcer in a sterile tube
or anaerobic system. Transport time is ≤2 hours.
a. Inner ear - Tympanocentesis should be reserved for
complicated, recurrent, or chronic persistent otitis media. For
intact eardrum, clean ear canal with soap solution and collect
fluid via syringe aspiration. Submit in sterile container. For
ruptured eardrum, collect fluid on flexible shaft swab via an
auditory speculum. Transport time <2 hours.
b. Outer ear - Use moistened swab to remove any debris or
crust from ear canal. Obtain sample by firmly rotating swab in
outer canal. For otitis externa, vigorous swabbing is required -
surface swabbing may miss streptococcal cellulitis.
a. Conjunctiva - Sample each eye with separate swabs
(premoistened with sterile saline) by rolling over conjunctiva.
When only one eye is infected, sampling both can help distinguish
indigenous microflora from true pathogens.
b. Corneal scrapings - Collected by ophthalmologist. Using
sterile spatula, scrape ulcers and lesions; inoculate scraping
directly onto media (BHI with 10% sheep blood, chocolate, and
inhibitory mold agar). Prepare 2 smears by rubbing material onto
1-2 cm area of slide. Transport time ≤15 min.
c. Vitreous fluid - Prepare eye for needle aspiration of
fluid. Transfer fluid to sterile tube. Transport time
K. Feces - see stool.
L. Fistula - see abscess.
M. Fluids - see sterile body fluids.
N. Genital - Cultures for Neisseria gonorrhoeae should
be collected using a Copan Liquid amies Elution Swab (ESwab).
Transport to laboratory immediately.
a. Endocervical - Remove cervical mucus with swab and
Insert a second swab into endocervical canal and rotate against
walls. Allow time for organisms to absorb onto the swab surface.
b. Urethral - Collect urethral specimens at least 1 h after
patient has urinated. Insert small swab 2-4 cm into urethral
lumen, rotate, leave for 2s to facilitate absorption.
O. Pilonidal cyst - see abscess.
P. Respiratory, lower - Transport time is ≤2 hours.
a. Bronchoalveolar lavage or brush, endotracheal aspirate -
Collect fluid in a sputum trap (907093); transfer to leak-proof
container (37777) for transport to microbiology laboratory; place
brush in sterile container with 1 mL saline.
b. Sputum, expectorated - Patient should rinse mouth and
gargle with water prior to collection; instruct patient to cough
deeply. Collect specimens in sterile transport containers
c. Sputum, induced - Have patient brush gums and teeth, then
rinse mouth thoroughly with water. Using a nebulizer, have the
patient inhale 20-30 mL of 3 to 10% sterile saline. Collect
sputum in sterile container.
d. If Nocardia is suspected, culture for Nocardia should be
requested as an add-on test as standard culture is inadequate
for its recovery.
Q. Respiratory, upper - Transport time ≤2 hours.
a. Oral - remove oral secretions and debris from surface of
lesion with a swab. Use a second swab to vigorously sample
lesion, avoiding normal tissue. Superficial swab specimens
should not be submitted. Tissue or needle aspirates are
b. Nasal swabs (R/O SAPCR) - Insert a sterile swab (use Copan
dual swab 26200) into the nose until resistance is met at the
level of the turbinates (approximately 1-2 cm into one nostril).
Rotate the swab against the nasal mucosa for 3 sec. Apply slight
pressure with a finger on the outside of the nose to ensure good
contact between swab and inside of nose. Using the same swab,
repeat for the other nostril.
c. Sinus aspirates - Aspirate with needle and syringe.
Cleanse rubber stopper of anaerobic transport vial (59546) with
alcohol; push needle through septum and inject specimen on top
d. Throat - Routine throat cultures will be processed only
for growth of β-hemolytic Streptococcus species.
Do not obtain throat samples if epiglottis is inflamed, as
sampling may cause serious respiratory obstruction. Sample the
posterior pharynx, tonsils, and inflamed areas with a Copan
Liquid Amies Elution Swab (ESwab).
R. Sterile body fluids (other than CSF) -
a. Transport fluid to laboratory in sterile, leak-proof container
(BD Vacutainer, no additive, yellow top, 924044) or anaerobic
transport vial (Vial, 59546).
b. Cleanse rubber septum of container with 70% alcohol. Allow
septum to dry for 1 min before inoculating.
c. Disinfect overlying skin with iodine or chlorhexidine
preparation. Obtain specimen with needle and syringe. Push
needle through septum of transport container and inject fluid.
d. Amniotic and culdocentesis fluids should always be transported
in an anaerobic transport vial (59546). Agar in anaerobic vial
should be clear before inoculation; inject fluid on top of agar.
e. Submit as much fluid as possible. NEVER submit a swab dipped in
fluid. NEVER inject fluid into swab container.
f. One aerobic blood culture bottle (924171) inoculated at bedside
(up to 10 mL) is highly recommended provided adequate sample is
available. If blood culture bottle is inoculated, submit separate
aliquot in anaerobic transport vial (59546) or sterile container
(924044) for preparation of cytocentrifuged Gram stain and
inoculation of solid media (allows quantitation, aids in culture
g. Transport time ≤15 min, room temperature.
S. Stool - Stools submitted on patients admitted for >3 days
will be rejected without prior preapproval (pager 4903 weekdays;
pager 3404 evenings and weekends). Submit 10-20 g in sterile
container. Transport time is ≤1 hour. Refrigerate if transport
is delayed. Stools are cultured to isolate bacterial causative
agents of diarrheal illness; Salmonella, Shigella, and
Campylobacter. Routine stool culture includes EIA
for Shiga toxin from E. coli. Cultures for Yersinia are
performed by special request. Stools for C. difficile
toxin detection must be transported to the laboratory immediately
or refrigerated if transport is delayed. Surveillance cultures may
be ordered on Bone Marrow transplant and other immunocompromised
patients to detect overgrowth of normal flora by Staph
aureus, yeast or a gram negative bacillus.
T. Tissue - Submit in anaerobic collection jar (59547) or
sterile screw-cap container (37777); add drops of sterile saline to
keep small pieces of tissue moist. Transport time ≤15 min.
U. Urine - Collect 4 mL of urine in a sterile specimen container
(37777). Transfer urine to a gray top C&S urine container. Tubes
must be filled to 3 mL do prevent inhibition of bacterial growth.
Transport to the microbiology laboratory. If unable to collect 3 mL
of urine, collect in sterile specimen container (37777) and
transport urine specimens to the Microbiology Laboratory or
refrigerate within 30 minutes. Refrigerated
specimens should be delivered to the lab as soon as possible, and
may be rejected if not received within 24 hours of collection.
Gray top C&S urine containers are not acceptable for urinalysis and
urine chemistries because the preservative interferes with testing.
Cultures can not be performed as an add-on test to urinalysis. Send
separate sample for urinalysis (random urine yellow top, round
bottom tube (no additive)) and culture (as above).
a. Midstream clean catch method: Patients should be
instructed to wash hands prior to collection and offered exam
1. Female patients should be instructed to sit
on toilet with legs apart and spread labia with one hand.
First void in toilet and then, continuing to void, hold
specimen container in "midstream" to collect sample.
2. Male patients should be instructed to retract
foreskin if uncircumcised. First void in toilet and then,
continuing to void, hold specimen container in "midstream" to
b. Straight catheter: Thoroughly cleanse the urethral
opening with soap and water. Rinse area with wet gauze pads.
Aseptically insert catheter into the bladder. After discarding
initial 15 to 30 mL of urine, collect 4 mL of urine for
submission in a gray top C&S urine container.
c. Indwelling catheter: Clamp catheter below port and allow
urine to collect in tubing. Disinfect the catheter collection
port with 70% alcohol. Use needle and syringe to aseptically
collect 4 mL freshly voided urine though catheter port.
Transfer to gray top C&S urine container. Do not collect urine
from collection bag.
d. Ileal conduit: Remove the external device and discard
urine within device. Gently cleanse the stoma with 70% alcohol
followed by povidone-iodine swab stick (907172). Using sterile
technique, insert a double catheter into the cleansed stoma, to
a depth beyond the fascial level, and collect the urine into a
sterile container. Transfer to gray top C&S urine container. Use
of a double catheter helps to minimize contamination of the
specimen with skin flora.
V. Wound - See abscess.