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 
               specified.
               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
                     obtained.
                  e. Deliver all specimens to the laboratory immediately after 
                     collection.
                  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
                     culture.
                     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
                        adequately decontaminated
               
               C. Blood
                  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
                        inoculating.
                     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 three initial sets of blood cultures sequentially from
                        separate phlebotomy procedures. Ideally, three venipunctures
                        should be performed immediately but a third set of bottles
                        can be drawn at a 4-6 hour delay without significant loss of
                        yield. (will detect >98% of BSIs).  
                     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 yellow top tube (104184).  Transport time <2
                  hours.
                  
               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.
               
                  Refer to the Microbiology Specimen Collection and Transport page
                  for orders placed per tube.
               
               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.
               
               I. Ear
                  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.
               
               J. Eye
                  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 
                     ≤15 min.
               
               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
                     discard.
                     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 
                     (37777).
                  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 
                     preferred.
                  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
                     of agar.
                  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
                     interpretation).
                  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).
                  a. Please use FecalSwabs [Stores #105117]. 1) Obtain a stool
                     specimen in a clean pan or container. Stool specimens should not
                     contain urine or water. 2) Holding FecalSwab shaft above the red
                     breakpoint mark, insert the entire tip of the FecalSwab into the
                     stool sample and rotate. Do not use FecalSwab as a spoon;
                     rather, coat swab with a visible layer. 3) If visible stool is
                     not coating the FecalSwab tip, reinsert until swab is coated.
                     4) Using swab and aiming tube away, mash and mix the stool
                     sample against the side of the tube to suspend the sample. 
                     5) Invert the tube several times to homogenize the sample and
                     expose the sample to Cary Blair preservative fluid.
                  b. The FilmArray Gastrointestinal Panel is a multiplex PCR
                     test capable of qualitatively detecting DNA or RNA of 22
                     pathogens (bacteria, parasites, and viruses). It requires a
                     FecalSwab.  The panel is used to diagnose infection caused by
                     Campylobacter species, Plesiomonas shigelloides,
                     Salmonella species, Vibrio species, V.
                     cholerae, Yersinia species, enteroaggregative E.
                     coli, enteropathogenic E. coli, enterotoxigenic
                     E. coli, Shiga toxin producing E. coli, E. coli
                     O157, Shigella/Enteroinvasive E. coli,
                     Cryptosporidium species, Cyclospora cayetanensis,
                     Entamoeba histolytica, Giardia lamblia, Adenovirus F 40/41,
                     Astrovirus, Norovirus, Rotavirus and Sapovirus.
                  c. Stools for C. difficile toxin detection must be
                     transported to the laboratory immediately or refrigerated if
                     transport is delayed.  This test requires raw stool, not a
                     FecalSwab.
                  d. 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.
                  e. Test of Cure Stool Culture (Salmonella, Shigella, EHEC) is
                     only for the listed organisms. For organisms other than these
                     please contact the Microbiology laboratory for approval.
                  f. Aeromonas Culture - Should be collected in FecalSwabs
                     (Stores #105117). This test may be added onto the FilmArray
                     Enteric Panel.
               
               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 
                     gloves.
                     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 
                        collect sample.
                  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.