Deliver all specimens to the laboratory as soon as possible after collection. 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 affect testing. Therefore, tests may be 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 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) c. A sterile container (37778) 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. Anaerobic swab (907464) - swab specimens are suboptimal, aspirate preferred. 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 skin with ChloraPrepChloraPrep® 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 two initial sets of blood cultures sequentially from separate phlebotomy procedures followed by a third and a fourth set at 4-6 hour intervals (will detect >99% of BSIs). Three sets of blood cultures collected within a 24 hour period will detect 96.9 - 98.3% 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 2007;45:3546). 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 - Prepare skin and bottles as for adult. Collect as much blood as possible up to 10 mL per bottle. 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 container (37778). 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 - Only intravascular catheter tips from pediatric patients and peritoneal dialysis catheters are routinely accepted for culture. Send 5 cm of distal tip in sterile screw-cap container (37778). Transport time is ≤15 min. Foley catheters are not accepted for culture since growth represents distal urethral flora. G. Cerebrospinal Fluid (CSF) - Aseptically collect CSF from a lumbar puncture into sterile tubes (907131). Send second tube (≥3 mL) to the Microbiology Laboratory. Transport time ≤15 min. Cerebrospinal fluid for bacterial culture should never be refrigerated. 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 with a sterile swab and inoculated directly to a Jembec plate (obtain from laboratory; place white tablet in hole of Jembec plate to provide CO₂ enriched atmosphere, close top of the plate tightly and place in Ziploc bag provided, keep at room temperature, deliver to lab as soon as possible). If a Jembec plate is unavailable, an aerobic culturette swab (922349) may be used if transported 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 (37778) for transport in pneumatic tube system); 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 (37778). 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. 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. Contact Microbiology Lab (356-2591) to arrange for provision of special media if culture for other organisms (Corynebacterium diphtheria, Neisseria gonorrhoeae) is desired. 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 sterile swab. 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 system (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 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 - 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, Campylobacter, and Shiga toxin producing E. coli. 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 (37778); add drops of sterile saline to keep small pieces of tissue moist. Transport time ≤15 min. U. Urine - Collect 1-10 mL of urine in a sterile specimen container (907069). 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. 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 urine for submission in a sterile 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 5-10 mL freshly voided urine though catheter port. Transfer to sterile 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. Use of a double catheter helps to minimize contamination of the specimen with skin flora. V. Wound - See abscess.