MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 1. Any amount but prefer > 1 ml. Any amount but prefer > 1 ml

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1 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 1 Abscess Remove surface exudate by wiping with sterile saline or 70% alcohol Syringe with needle removed or Sterile cup or Eswab device, Eswab (not preferred but acceptable) Any amount but prefer > 1 ml <2 h, RT <2 h, RT <24 h, RT Tissue or fluid is always superior to swab specimen. More than 1 culture accepted per day if deemed necessary by the surgical OR group Abscess closed Aspirate abscess wall material with needle and Aseptically transfer material into transport s. Syringe with needle removed or Sterile cup or Eswab device or Eswab (not preferred) Any amount but prefer > 1 ml <2 h, RT <2 h, RT <24 h, RT Tissue or fluid is always superior to swab specimen. More than 1 culture accepted per day if deemed necessary by the surgical OR group Blood Culture See separate collection guidelines BACTEC Peds Plus BACTEC Lytic See collection guideline <2 h, RT <2 h, RT Not applicable 3 sets in 24 h Acute sepsis: 2-3 sets from separate sites, all within 10 minutes is optimal Endocarditis: 3 sets from 3 sites over 1-2 hours Fever of unknown origin: 2-3 sets from separate sites >1 h apart See also Compliance 360 Nursing Procedure NUR 1014 Catheter IV tip Cleanse skin around catheter site with 70% alcohol. Aseptically remove and clip 5 cm distal tip of catheter directly into sterile cup. Transport directly to laboratory to prevent drying. Sterile screw cup Not applicable Not applicable < 15 min, RT < 15 min, RT < 2 h, 4 C None IV catheters for semi quantitative culture: Central line, CVP, Hickman, Broviac, peripheral, arterial, umbilical, hyperalimentation, Swan-Ganz Catheter Foley Do not culture since growth represents distal urethral flora. Not acceptable for culture Cellulitis, aspirate Cleanse skin around catheter site with 70% alcohol. Aseptically aspirate the area of maximum inflammation (commonly the center rather than the edge) with a needle and Irrigation with a small amount of sterile saline may be necessary. Sterile screw tube or cup; syringe transport not recommended device, Eswab (not preferred but acceptable) Any amount but prefer > 1 ml < 15 min, RT < 15 min, RT < 24 h, 4 C None Yield of potential pathogens in minority of specimens cultured

2 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 2 CSF Disinfect site with iodine or chlorohexidine preparation. Insert a needle with a stylet at L3-L4, L4,L5 or L5- S1 interspace. Upon reaching the subarachnoid space, remove the stylet and collect 1-2 ml of fluid into each of three leakproof tubes (if sufficient fluid available). Sterile screw cap tube (s) Not applicable Bacterial, > 0.5 ml (prefer > 1 ml) Fungi, 1 ml AFB, > 2 ml Viral, > 2 ml < 15 min, RT Not applicable None Obtain blood cultures also. If only 1 tube of CSF collected, submit to Microbiology laboratory first. Note, if CSF is from a shunt patient please indicate in orders. Decubitus ulcer A swab is not a specimen of choice. Cleanse surface with sterile saline. If sample biopsy is not available, aspirate inflammatory material from the base of the ulcer. Sterile screw cup, tube. Eswab accepted, but not preferred device preferred; Eswab accepted but not preferred. Any amount but prefer > 1 ml <2 h, RT <2 h, RT <24 h, RT Since a swab specimen of a decubitus ulcer provides no clinical information, it should not be submitted. A tissue biopsy sample or needle aspirate is the specimen of choice. Dental culture: gingival, periodontal, periapical, Vincent's stomatitis Carefully cleanse gingival margin and supragingival tooth surface to remove saliva, debris, and plaque. Using a periodontal scaler, carefully remove subgingival lesion material and transfer to an anaerobic transport device. Not applicable device preferred; Eswab accepted but not preferred. Not applicable <2 h, RT <2 h, RT <24 h, RT Ear Inner Tympanocentesis reserved for complicated, recurrent, or chronic persistent otitis media. For intact ear drum, clean ear canal with soap solution and collect fluid in a syringe aspiration technique (tympanocentesis). Sterile tube device preferred; Eswab accepted but not preferred. Not applicable <2 h, RT <2 h, RT <24 h, RT Results of throat or nasopharyngeal swab cultures are not predictive of agents responsible for otitis media and should not submitted for that purpose. Laboratory Note: Please indicate that the source is tympanocentesis. Ear Outer Use a moistened swab to remove any debris or crust from the ear canal. Obtain a sample by firmly rotating swab in the outer canal. Eswab Not applicable <2 h, RT <2 h, RT <24 h, RT For otitis external, vigorous swabbing is required since surface swabbing may miss streptococcal cellulitis.

3 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 3 Eye Conjunctiva Sample both eyes with separate swabs (premoistened with sterile saline ) using a mini flocked swab by rolling over each conjunctiva. Label each individual swab as left and right eye appropriately. Eswab, mini flocked swab with green top Not applicable <2 h, RT <2 h, RT <24 h, RT None If possible, sample both conjunctiva, even if only one is infected, to determine indigenous microbiota. The uninfected eye can serve as a control with which to compare the agents isolated from the infected eye. If cost prohibits this approach, rely on the Gram stain to assist in interpretation of culture. Eye Corneal scrapings Specimen is collected by an ophthalmologist. Using a sterile spatula, scrape ulcers or lesions, and inoculate Inoculated media or scraping directly on media received from flocked ESwab the Microbiology Laboratory. Prepare smears by rubbing material from spatula onto 1 - to 2 cm area of slide. Not applicable < 15 min, RT < 15 min, RT None If conjunctival specimen is collected, do so before anesthetic application, which may inhibit some bacteria. Corneal scrapings are obtained after anesthesia. Include fungal culture requests. Scrapings for virus isolation and ameba detection should be submitted in a sterile. Eye vitreous fluid aspirates Prepare eye for needle aspiration of fluid Sterile screw cap tube Not applicable < 15 min, RT <2 h, RT Not Applicable Include fungal request. Anesthetics may be inhibitory to some etiologic agents. Feces Routine culture Pass specimen directly into a clean, dry. Do not submit a diaper. Transport immediately to the laboratory if specimen is not placed in preservative wide-mouth cup or Cary Blair medium d: < 1 h, RT Holding medium: < 24 h < 24 h, 4 C <48 h, RT or 4 C 1 per day Do not perform routine stool cultures for patients whose length of hospital stay is >3 days. Test for C. difficile should be considered for these patients. See rectal swab for collection information. Feces, C. difficile Pass liquid or soft stool directly into a clean, dry. Formed stool not acceptable for testing. wide-mouthed < 1 h, RT 1-24 h, 4 C 2-3 days - 70 C Not applicable 1 per day. No repeat testing if patient previously positive within 7 days. Patients should be passing 3 ml of liquid or soft stools per 24h. Formed or hard stool will be rejected. Feces E. coli (O157:H7) and other Shiga toxin producing serotypes Pass liquid or bloody stool into a clean, dry. wide-mouth cup or Cary Blair medium d: < 1 h, RT Eswab: 24h, RT or 4 C Eswab: 24h, RT or 4 C 24h, RT and 4 C 1 per day

4 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 4 Feces Leukocyte detection Send in clean, dry. wide-mouthed < 1 h Not applicable Not applicable 1 per day Controversial: some believe this procedure provides results of little clinical value. Feces, Ova & Parasite Pass specimen directly into a clean, dry. Do not submit a diaper. Transport immediately to the laboratory if specimen is not placed in preservative. If any delay in transport, inoculate Total Fix vial. Total Fix d: < 1 h, RT Holding medium: < 24 h Holding medium: < 24 h 1 per day Feces Rectal swab 1. Carefully insert a swab approximately inches beyond the anal sphincter. 2. Gently rotate the swab to sample the anal crypts. 3. Feces should be visible on the swab for detection of diarrheal pathogens. Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT 1 per day Reserved for detecting N. gonorrhoeae, anal carriage of betahemolytic Streptococcus, or for patients unable to pass a specimen. Rectal Swab For GC/Chlamydia Probe Collection Procedure Rectal Collection Device.docx Not applicable 2 h, RT Feces, for Rotavirus or Adenovirus 40/41 Send in clean, dry. wide-mouthed < 2 h, RT Not applicable < 24 h, 4 C 1 per day Fistulas See Abscess Fluids (abdominal, ascites, bile, joint, pericardial, peritoneal, pleural, synovial) 1. Disinfect overlying skin with iodine preparation. 2. Obtain specimen via percutaneous needle aspiration or surgery. 3. Submit as much fluid as possible; never submit a swab dipped in fluid. Sterile screw-cap tube or capped > 1 ml 15 min, RT 15 min, RT 24 h, RT Pericardial fluid and fluids for fungal cultures, <24 h, 4 C none Fluids are best examined by Gram staining of a cytocentrifuged preparation. Inoculation of a blood culture bottle is highly recommended. For more information on obtaining peritoneal dialysis fluid, see Compliance 360 PD Gangrenous tissue See Abscess

5 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 5 Gastric Wash or lavage for mycobacteria Collect in early morning before patients eat and while they are still in bed. 1. Introduce a nasogastric tube into the stomach. 2. Perform lavage with ml of chilled sterile, distilled water. 3. Recover sample and place in a leakproof, sterile. Prefer > 1 ml 15 min, RT or neutralize within 1 h of collection 15 min, RT or neutralize within 1 h of collection 24 h, 4 C The specimen must be processed promptly, since mycobacteria die rapidly in gastric washings. Neutralize when holding for >1 h with sodium bicarbonate. Gastric biopsy for H. pylori Collected by gastroenterologist during endoscopy. Not applicable Culture may be needed for antimicrobial testing. Amniotic fluid Aspirate via amniocentesis. or capped syringe > 1 ml 2 h, RT Not applicable 24 h, RT none Swabbing or aspiration of vaginal secretions is not acceptable because of the potential for contamination with commensal vaginal biota. Bartholin gland secretions Cervical secretions Cul-de-sac fluid Endometrial tissue and secretions 1. Disinfect skin with iodine preparation. 2. Aspirate fluid from ducts. 1. Visualize the cervix using a speculum without lubricant. 2. Remove mucus and secretions from the cervical with swab and discard the swab. 3. Firmly yet gently sample the endocervical canal with a new sterile swab. Submit aspirate or fluid 1. Collect transcervical aspirate via a telescoping catheter. 2. Transfer entire amount to proper collection s. or capped syringe > 1 ml 2 h, RT Not applicable 24 h, RT none Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT or capped syringe or capped syringe > 1 ml 2 h, RT 2 h, RT 24 h, RT > 1 ml 2 h, RT 2 h, RT 24 h, RT Collection and transport will differ for C. trachomatis.

6 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 6 Urethral secretions Collect at least 1 h after the patient has urinated. 1. Remove old exudate from the urethral orifice. 2. Collect discharge material on a swab by massaging the urethra against the pubic symphysis through the vagina Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT If no discharge can be obtained, wash the periurethral area with povidoneiodine soap and rinse with water. Insert a small swab 2-4 cm into the urethra, rotate swab, and leave swab in place for at least 2 seconds to facilitate absorption. Urethral secretions (endocervical for GC/Chlamydia Probe) Collection Procedure for GC/Chlamydia probe Endocervical Swab Not applicable 2 h, RT Vaginal secretions 1. Wipe away old secretions/discharge. 2. Obtain secretions from the mucosal membrane of the vaginal wall with a sterile swab or pipette. 3. If a smear is also needed, use a second swab. Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Gram stain, not culture, is recommended for the diagnosis of BV. Eswab acceptable transport for Neisseria gonorrhoeae culture. Vaginal secretions for GC/Chlamydia Probe Vaginal Probe Collection Vaginal probe collection device Not applicable 2 h, RT Vaginal secretions for Trichomonas culture or male lesion Genital: Urethral secretions Trichomonas culture collection 1. Clean with sterile saline and remove lesion's surface with a sterile scalped blade. 2. Allow transudate to accumulate. 3. While pressing the base of the lesion, firmly rub base with a sterile swab to collect fluid. Collect at least 1 h after patient has urinated. 1. Remove old exudate from urethral orifice 2. Collect discharge material on using a flocked swab (Eswab) by massaging the urethra against the pubic symphysis Trichomonas Culture Collection Pouch.docx Not applicable 2 h, RT 2 h, RT 24 h, RT Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT If no discharge can be obtained, wash the periurethral area with providoneiodine soap and rinse with water. Insert a small swab 2-4 cm into the urethra, rotate swab, and leave swab in place for at least 2 seconds to facilitate absorption

7 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 7 Genital Male Urethral for GC/Chlamydia Probe Procedure for GC/Chlamydia probe Endocervical Swab Not applicable 2 h, RT Genital Male Urethral for Neisseria gonorrhoeae culture Collection Procedure for GC/Chlamydia probe Mini-tip Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Genital - Male prostate Pilonidal cyst 1. Cleanse the urethral meatus with soap and water. 2. Massage the prostate through the rectum. 3. Collect fluid expressed from the urethra on a sterile flocked swab. See Abscess Mini-tip Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Respiratory, lower Bronchoalveolar lavage, brush, or wash; endotracheal aspirate 1. Collect washing or aspirate in a sputum trap. 2. Place brush in sterile with 1 ml of saline Sterile cup >1 ml; If multiple test requests >5 ml of fluid is required 2 h, RT Not applicable 24 h, RT * *Multiple specimens may be submitted from different lung sites from bronchoalveolar lavage For more information on collection, see Compliance 360 Nursing procedure NUR.0913 Respiratory Sputum, expectorated 1. Collect specimen under the direct supervision of a nurse of physician. 2. Have patient rinse or gargle with water to remove excess oral biota. 3. Instruct patient to cough deeply to produce a lower respiratory specimen (not postnasal fluid). 4. Collect in a sterile. Sterile cup Prefer > 1 ml 2 h, RT 2 h, RT 24 h, RT For more information on collection, see Compliance 360 Nursing procedure NUR.0913 Respiratory Sputum, induced 1. Collect specimen under the direct supervision of a nurse or physician or respiratory therapist 2. Have patient rinse or gargle with water to remove excess oral biota. 3. Instruct patient to cough deeply to produce a lower respiratory specimen (not postnasal fluid). 4. Collect in a sterile. Sterile cup Prefer > 1 ml 2 h, RT 2 h, RT 24 h, RT For more information on collection, see Compliance 360 Nursing procedure NUR.0913

8 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 8 Respiratory, Deep throat Deep throat cultures are usually collected on children with Cystic Fibrosis who are too young to produce sputa. Have patient rinse mouth to remove excess oral biota. Have the patient cough deeply and swab back of throat with flocked swab. Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Deep throat specimens are only accepted from patients with Cystic Fibrosis for routine culture. If additional testing is requested (AFB or Mycology, send an additional Eswab. Respiratory Upper, Oral Remove oral secretions and debris from the surface of the lesion with a swab. Discard this swab. Using a 2nd swab, vigorously sample the lesion, avoiding any areas of normal tissue. Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Sampling of superficial tissue for bacterial evaluation is discouraged. T issue biopsy specimens or needle aspirate are the specimens of choice. Respiratory, Nasal Insert a flocked swab approximately 1-2 cm into the nares. Rotate the swab against the nasal mucosa. If collecting for MRSA surveillance, repeat process for each nares with the same swab. Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT Anterior nose cultures are reserved for detection staphylococcal carriers or for nasal lesions Respiratory, Nasopharynx Respiratory, throat or pharynx Respiratory, throat or pharynx for GC/Chlamydia Probe Stool, see Feces Tissue Gently insert a small swab (e.g., mini tipped flocked swab into the posterior nasopharynx via the nose. 1. Depress tongue with a tongue depressor 2. Sample the posterior pharynx, tonsils, and inflamed areas with BD red top swab 1. Depress tongue with a tongue depressor 2. Sample the posterior pharynx, tonsils, and inflamed areas with BD red top swab Collected during surgery or cutaneous biopsy procedure Eswab Not applicable 2 h, RT 2 h, RT 24 h, RT BD EZ red top swab Not applicable 2 h, RT 2 h, RT 24 h, RT Pharyngeal or throat Collection Device for GC/Chlamydia Probe Screw-cap. Add several drops of Anaerobe transport sterile saline to system keep small pieces of tissue moist. Not applicable 2 h, RT Not applicable <15 min, RT <15 min, RT 24 h, RT Not applicable Throat swabs are contraindicated in patients with epiglottis. Swabs for N. gonorrhoeae should be placed in Eswab. Submit as much as possible. If there is excess tissue, save a portion of surgical tissue at -70 C in case further studies are requested.

9 MICROBIOLOGY SPECIMEN COLLECTION AND TRANSPORT GUIDELINES 9/22/2015 Page 9 Urine for GC/Chlamydia probe (NAAT) testing Male and female should use the first voided specimen of the day Sterile urine >5 ml d: < 2 h, RT 2 h, RT 24 h, 4 C NAAT testing for GC/Chlamydia is not suitable for add-on testing on specimens that have already been processed in the laboratory Urine, Female midstream Urine, straight catheter 1. While holding the labia apart, begin voiding. 2. After several milliliters has passed, collect a midstream portion without stopping the flow of urine. 3. The midstream portion is used for bacterial culture. 1. Thoroughly cleanse the urethral opening with soap and water. 2. Rinse area with wet gauze pads. 3. Aseptically, insert catheter into the bladder 4. After allowing approx. 15 ml to pass, collect urine to be submitted in sterile. Sterile, widemouthed ; or urine transport tube with boric acid Sterile, widemouthed ; or urine transport tube with boric acid > 1 ml preferred > 1 ml preferred d: <2 h, RT d: <2 h, RT 24 h, 4 C 24 h, 4 C Cleansing before voiding does not improve urine specimen quality; midstream urine samples are equivalent to clean-catch midstream urine samples For additional guidelines, see Compliance 360 NUR 0914 For additional guidelines, see Compliance 360 NUR 0914 Urine, Indwelling catheter 1. disinfect the catheter collection port with 70% alcohol. Clamp catheter below Sterile, widemouthed ; port and allow urine to collect tin tubing for minutes. or urine transport 2. Use needle an syringe to aseptically tube with boric acid collect 5-10 ml of urine > 1 ml preferred d: <2 h, RT 24 h, 4 C For additional guidelines, see Compliance 360 NUR 0914 Wound See Abscess